Chapter 1

_____________________________________________________Introduction______ 1.

Introduction:

1.1 Cyanobacteria: The cyanobacteria are an ecologically, morphologically, and physiologically diverse group of organisms whose primary productivity contributes to the bioenergetic foundation for higher trophic levels in marine, freshwater and terrestrial environment.

Ecologically cyanobacteria are not only capable of

modifying their habitat through fixation of atmospheric N2 but also capable of producing biologically active natural products [3]. Cytologically they resemble Gram negative bacteria, but their mode of nutrition is photoautorphic. Like higher plants

they

possess

chlorophyll

a

and

water

soluble

red

and

blue

phycobiliproteins as well as phtosystem I and II, hence they can use water for photosynthesis and produce oxygen, which subsequently released into the atmosphere.

Along with this beneficial part of cyanobacteria they were also

known to produce toxins. Published account of field poisoning by cyanobacteria were documented since the late 19th century[4].

These reports describes

sickness and death of livestock, pets and wildlife following ingestion of water containing toxic algae cells or the toxins released by ageing cells. Most recent reports on such incidents were given by several authors[5-9].

Primarily, two

types of toxins, hepatotoxins and neurotoxins have been characterized from these cyanobacteria. About 50% of Microcystis waterbloom shows hepatotoxicity to mammals and other animals.

The chemical investigation of marine cyanobacteria for their unique natural products began with the pioneering work of Richard Moore at the University of Hawaii. In the early 1970ʼs his laboratory published several surveys of marine cyanobacteria from the Pacific showing that they were rich in potential anticancer and antiviral substances[10,11]. These investigations also include several path-

_____________________________________________________Introduction______ breaking structure elucidations of these toxins.

The ecological roles played by

these toxins for cyanobacteria is that of anti-grazing mechanism, to fend off phytoplankton grazers in marine and freshwater environments[12].

In addition to toxins, cyanobacteria produce compounds of pharmaceutical interests. The genus Nostoc GSV224 produce cryptophycin, a potent inhibitor of microtubule assembly, which shows anticancer properties against various types of tumors including that of multi-drug resistant tumors.

The genomic revolution has changed the face of natural product research. Over the last two decades, more than 150 complete biosynthetic gene clusters from bacteria, fungi and plants have been characterized[13].

Recent investigations

over the past 15 years into the genetics studies of secondary metabolites provided an explosive impetus to the field of natural product synthesis. This molecular prospective has focussed on some of the most pharmaceutically useful and structurally diverse microbial metabolites belonging to the classes of polyketide synthase (PKSs) and nonribosomal peptide synthetases (NRPs). Because of the development of molecular approaches, there is growing trend towards using the molecular genetics to identify biosynthetic pathways and novel enzymes.

The principal pioneer in this area was Sir David Hopwood who

identified genes encoding for the biosynthesis of actinorhodin[14]. The genes were sequenced (a formidable task during those days) and the primary sequence of the various proteins was established.

_____________________________________________________Introduction______ Table____: Sequenced cyanobacterial NRPS/PKS gene clusters

Gene bank accession no

Cyanobacterial strain

compound

AJ269505, AJ536156

Anabaena Strain 90

Anabaenapeptolide[15,16] Microcystin[16]

AF516145, AY652953

Lyngbya majuscula strain 19L

Barbamide[17], Curacin[18]

AY522504

L. majuscula strain JHB,

Jamaicamide[19], lyngbyatoxin[20]

AF183408,

Microcystin[21], [22]

AJ441056

Microcystis aeruginosa PCC 7806, M. aeruginosa K-139 Planktothrix agardhii CYA126

AF204805, AY167420

Nostoc GSV224, Nostoc ATCC 53789

Nostopeptilide [24], Nostocyclopeptide[25]

Microcystin[23]

Table 1: Some important bioactive compounds isolated from marine and freshwater cyanobacteria (as of January 2007) Organism

Class of compound

Bioactivity

Chemical nature

Reference

Microcystis Sp

Lipopeptide

Cytotoxic

Toxin

[26]

Microcystis aeruginosa

Lipopeptide

Enzyme inhibitor, cytotoxic, tumor promoter, anticancer,

Aeuroginisin, kawaguchipeptin, microcystin, microviridin,

[7,27,28]

Synechocystis trididemni

Lipopeptide

Anticancer, antiviral, immunosuppressive

Didemnin

[29-32]

Lyngbya majuscula

Alkaloids, imidazole, lipopeptides

anticancer, antifungal, antimicrobial, antiviral, antiinflammatory, neurotoxic, skin irritant, toxin, antigrazers, alkaline phosphatase activity, antifeedant, neurotoxin, cytotoxic

[19,33-55]

Lyngbya lagerheimii Oscillatoria acutissima Phormidium tenue

Sulfolipid lipopeptide

Anti-HIV Antineoplastic agent

Fatty Acid (sulfolipid)

Anti-HIV

Dolastatin, Lyngbyabellin B, microcolin A laxaphycins A and B, homodolastatin 16 Curacin A, lyngbyabellins A and B, Aurilides B and C, kalkitoxin Lyngbyatoxins B and C Fatty Acid (Sulfo) Acutiphycin and 20,21didehydroacutiphycin sulfolipid

Spirulina platensis Anabaena flos-aquae

Lipopeptide

Anti-HIV, Radical Scavenger, hematopoietic antibiotic, anticancer

[56] [57] [58] [59-62]

alkaloide, lipopeptide

[63-65]

_____________________________________________________Introduction______ Aulosira fertilissima Calothrix sp. Cylindrospermum licheniforme Cylindrospermopsis raciborskii Nodularia spumigena Nostoc sp.

Aromatic Indoles Alkaloid

Anticancer Antimalarial, anticancer Anticancer, cytotoxic

Aulosirazole Calothrixin Cylindrocyclophane

[66] [67] [68]

Alkaloid

Cytotoxic

Cylindrospermopsin

[69]

Lipopeptide Amide, lipopeptide

Enzyme inhibitation Anticancer, cytotoxic, antifungal, antibiotic

[70-72] [73,74]

Nostoc commune

Lipopeptide, terpene, oligosaccharide Peptide and proteins Lipopeptide

Antifungal, antibiotic, antimitotic, cytotoxic

nodularia toxin Cryptophycin, nostophycin, nostocyclamide, nostocyclin Nostodione, microsporine, diterpenoid

Anti-HIV, antiviral

Cyanovirin

[77,78]

Cytotoxic, antifungal, antiviral

Halichondrin, scytophycin

[79,80]

Sulfolipids

Anti-HIV, anticancer

monogalactopyranosyl glycerol (MGG) and digalactopyranosyl glycerol (DGG)

[58]

Nostoc ellipsosporum Scytonema pseudohofmanni Phormidium tenue

1.2

[75,76]

Cyanobacterial Non-Ribosomal Peptides:

Despite increasing interest and perceived value of cyanobacterial secondary metabolites, only few biosynthetic studies have been completed (table __)[81,82]. Consequently, very little has been known about the molecular mechanism and biochemistry of these fascinating pathways responsible for the production of these secondary metabolites. Some important noteworthy studies done in this regard[18,20,21,25,83-86] but most of the studies were restricted to few representative species, hence it has been stressed that cyanobacteria are the most unlucky organisms having great potential and economic values but poorly characterized[87].

Generally, it has been considered that secondary metabolites are usually produced during stationary phase of microbes but cyanobacteria produces bioactive peptides in all

growth phases[88], but depending upon the growth

phase different metabolites may be produced in different concentration[88].

It has been a well-established fact that majority of peptide bond formation is catalysed by ribosomes, and generally the catalytic activity of peptide bond

_____________________________________________________Introduction______ formation by nonribosomal peptide synthetases (NRPS) has been largely overlooked. The list of molecules synthesized through NRPS is enormous[89] such as vancomycin, which is considered as the last resort, produced by NRPS and associate enzymes[90].

Molecules made by NRPS are generally cyclic, have high density of high proteinogenic amino acids and these amino acids are often connected by bonds other than peptide and disulphide bonds. NRPS are known to be very large proteins and consists of series of repeating enzymes fused together. Such fusion of repeating enzymes in a single polypeptide is similar to that of protein machinery responsible for polyketide biosynthsis (PKS)[91]. In NRPS, one amino acid building block is incorporated into the peptide product by each module, hence products with 15 amino acids would be expected to be constructed by an NRPS with ten modules stitched together. This is called as Structural Colinearity. Each module is normally specific to a particular amino acid substrate but this rule has exceptions particularly for siderophores[92,93].

Structurally, NRPS are

organized into modules, each of the modules are responsible for one cycle of elongation by the incorporation of single amino acid into the chain.

Each

elongation module consists primarily of three basic domains: adenylation, thiolation and condensation.

The adenylation domain (A) selects a specific

amino acid and activates it as an amino acyl adenylate. The activated amino acid is then transferred to phosphopantethiene group of the peptidyl carrier protein (PCP) or thiolation domain (T). Condensation domain (C) catalyze the peptide bond formation between amino acid in adjacent module. The chain is elongated successively and released at the end by the action of thioesterase domain (TE). Apart from these basic modules, which are ubiquitously present,

_____________________________________________________Introduction______ there also present certain tailoring/ accessory modules which certainly adds to the structural diversity such as epimerization (E), N-methylation (MT), cyclization (Cy), oxidoreductase (Ox), N-formylation (F), and reductase (R)[94].

These

domains helps to incorporate diverse amino acid functionality such as thiozoles, oxazolidones, oxazoles, thiozolidines as well as other functionality like Nmethylation and D-amino acids generally not found in any other system in nature [94].

Main Functional domains of NRPS Modules: A large number of therapeutically useful cyclic and linear peptides of bacterial or

Figure___: Reaction catalyzed by the NRPS domains. Reaction catalyzed by principal domains A, PCP, C & TE is given along with other auxiliary domains such as E, Cy, F, Ox, R, and N-Mt-domains. (taken from Schwarzer et al.[1])

fungal origin are synthesized via a template-directed, nucleic-acid-independent nonribosomal mechanism. This process is carried out by mega-enzymes called

_____________________________________________________Introduction______ nonribosomal peptide synthetases (NRPS).

NRPS are organized as iterative

modules, one for each amino acid to be built into the peptide product. Generally the modules are colinear to the sequence of the synthesized peptide, thus providing a linear workflow for the peptide synthesis[95,96].

A typical module comprises

1000 residues and is responsible for one reaction

cycle of selective substrate recognition and activation as adenylate, covalent intermediate fixation in the form of enzyme-bound thioester, and peptide-bond formation. A minimal elongation module consists of a 55 kDa adenylation (A) domain, responsible for substrate selection and activation through ATP hydrolysis [97,98], a 10 kDa downstream peptidyl carrier protein (PCP) domain for the covalent fixation as a thioester [99], and a 50 kDa condensation (C) domain,

located upstream of the A domain [100] which catalyzes the peptide-bond formation between an activated aminoacyl-bound intermediate and a peptidylbound intermediate of two adjacent modules. The result is a peptide elongated by one residue fixed to the PCP domain and the regeneration of the PCP domain in the preceding module. The basic set of domains within a module can be extended

by

domains

such

epimerization,

optional as

modification domain

N-methylation,

for and

heterocyclic ring formation — which are

Taken from Weber and Marahiel [2]

inserted at specific locations in the module [89].

This enlarges the broad

spectrum of possible products that results from the incorporation of non-

_____________________________________________________Introduction______ proteinogenic substrates such as carboxylic acid(for example, over 100 carboxylic acids are known as substrates). Further diversity is also achieved through product cyclization and post-assembly modifications [101]. In its modular organization, nonribosomal peptide synthesis resembles fatty acid synthesis (FAS) and polyketide synthesis (PKS), which are both carried out on similarly organized multienzyme complexes[102,103]. Furthermore, in all three cases the cofactor used for intermediate fixation and downstream transport is a 4′phosphopantetheine (4′PP) moiety. This moiety is linked to a serine residue of the PCP domain, the acyl carrier proteins (ACPs) of PKS and FAS. The cofactor is derived from coenzyme A and post-translationally attached to the apoenzymes of all three families by dedicated 4′PP-transferases [104].

Adenylation Domain: Adenylation domain catalyzes the specific activation of carboxyl group of amino acid, imino acids or hydroxyl acids. Each adenylation domain has a specific geometry of binding pocket which only allows a specific amino acid to enter into the catalytic site. The analysis of phenylalanine binding pocket of the first module of the Bacillus brevis Gramicidin S synthetase I (GrsA) has led to the prediction of substrate in NRPS adenylation domain[104].

The adenylation domain was

expressed as a single domain and codes for the initiation module at the putative domain border between the A and PCP domain.

The A domain has same

homology in its chemistry that of ribosomal pathway aminoacyl tRNA but has no sequence homology to the tRNA. The phenylalanine-activating domain (PheA) consists of two subdomains, a smaller C-terminal subdomain of ~100 residues and a larger 400 residue N-terminal subdomain A (figure___). Adenylation of the substrate amino acid (aa2) leads to aminoacyl-adenylate (aa-AMP reaction) which

_____________________________________________________Introduction______ is non-covalently attached to the A-domain (red). The thiol group of the 4’PP cofactor of the PCP domain (green) accepts the activated substrate. In the next step is the formation of first peptide bond which is catalyzed by the C domain (grey) which is present upstream to the A domain.

The presentation of the

loaded cofactor of the PCP domain to a nucleophile acceptor position “a” and delivery of the corresponding thioester-bound amino acid of the preceding module (aa1) to an electrophile donor position “d” of this C domain are necessary for the reaction to take place. The result of this reaction is the formation of an elongated peptide loaded on to the PCP domain and recycling of the upstream PCP thiol group. The peptide linked to the PCP domain is then translocated to the third position to be served, the electrophile donor position of the downstream C domain. The second pepbond bond is formed here (reaction 4) with the amino acid activated by the following A domain (aa3) which is fixed to the corresponding downstream PCP. After completion of this reaction cycle, the growing peptide chain is attached as a thioester to the PCP domain of the following module adopts a regenerated status (thiol). The 4'PP cofactor of the PCP domain is shown in the three positions that have to be served; there is only one cofactor for each module attached to the PCP domain.

The main difference between the ribosomal and nonribosomal systems is the application of an accurate proofreading mechanism for ribosomal protein synthesis but however nonribosomal synthesis shows less stringent substrate selection and incorporation[105]. Because of the multiple carrier thiotemplate mechanism and because of the presence of A domain for each residue added into the growing peptide chain a relative relaxed substrate selectivity has been observed. On the other hand in ribosomal peptide synthesis substrate selectivity

_____________________________________________________Introduction______ is relatively stringent and hence the incorporation of amino acid is highly controlled[106]. The relaxed substrate specificity of A domain can be further supported from the studies of Dieckmann[107] in his ATP-ppi exchange assay. For example, BarD, it incorporate L-leucine but activates 3-chloroleucine and valine as well[17].

The leucine specific adenylation domain of McyB of

Microcystis aerugionsa activates isoluecine and valine[108]. Similirly, the first A domain of NosA activates Val, Ile and Leu when expressed in E. coli, but Leu is not present in nostopeptolide[24]. In cyanobacteria, as many as 200 adenylation domains have been identified so far. system.

They are generally present in NRPS

Upon alignment, 10 core motifs (A1-A10) are highly conserved in

cyanobacterial NRPS systems which are also found in fungal system[109].

Peptidyl Carrier Protein(PCP) / Thiolation Domain (T): This is the second domain generally found immediately after the A domain. The key role of these domains is in the transport of intermediates, which require specific interactions with the activating A domain and the corresponding C domain for aminoacyl and peptidyl elongation cycle. These domains also work in collaboration with other auxiliary domains for intermediate modifications. This thiolation

domain

require

interactions

with

epimerization

domain,

methyltransferase domain, oxidation domain, reduction domain, or with thioesterase domain in the terminal cyclization reaction[2]. The thiolation domain (T) is also called as Peptidyl Carrier Protein (PCP). Its function is more or less similar to that of ACP (acyl carrier protein) of the PKS system. Although ACP and PCP are functionally similar, they show little homology except at the cofactor binding site which has a signature sequence LGx(HD)SL[96].

Both of them

activates their substrate as acyl adenylate and fix them for further treatment as a

_____________________________________________________Introduction______ thioester to the 4 ‘PP cofactor of the carrier protein[110,111]. Besides the PCP domain structure, the NMR structures of prototypes for FAS ACPs and PKS ACPs are known. All three carrier proteins (FAS ACP, PKS ACP, and PCP) consists of approximately 80 residues and are composed of a distorted antiparallel four-helix bundle with a long loop between the first two helices (fig: ___). The serine residue which is the site of cofactor binding is located at the junction between loop and the second helix.

Serine Residue Cofactor binding pocket

Fig_____: Similarity of PCP Domains to Acyl Carrier Proteins: Cartoon structure of (a) the NRPS PCP domain (PDB code 1DNY), (b) the fatty acid synthase ACP (PDB code 1ACP), and (c) The primary role domain inserine theresidues transport ofcofactor are the actinorhodin polyketide synthaseof ACP PCP (PDB code 1AF8). Theis invariant that carry the 4′PP highlighted in ball-and-stick format. The similarity of the overall fold as well as differences in lengths and relative orientations of intermediates which are activated by the adenylation domain the helices between these members of the same protein family are apparent. (The figure was taken from Weber& Marahiel[2])

and subsequent interaction with the condensation domain for aminoacyl and peptidyl elongation cycle[112]. Condensation Domain (C):

This domain is the third domain present in the NRPS system. It catalyze the elongation reaction of peptidyl chain which is tethered to the phosphopantetheinyl arm of the T/PCP domain (which is present upstream) to the amino acid bound to the downstream T domain[113]. This is the reason the first module usually do not contains C domain but the second module has the domain sequence CAT (Condensation—Adenylation—Thiolation).

Thus it can be said that the C

domains are inserted between each consecutive pair of activating units (which may include additional auxillary domains such as E, N-Met) (Fig: ___). This

_____________________________________________________Introduction______ arrangement resembles the basic setup for the sequential linkage of activating amino acids to synthesize a linear peptide. Thus it can be said that the number of C domains found in bacterial peptide synthetase system corresponds with the number of the linear intermediates[96]. Not much information has been available for the C domain up until now. According to Raush[114], there exists 7 functional subtypes of the C domain: i) A LCL domain which catalyzes peptide bond formation between two L-amino acids. ii) DCL domain which links an L-amino acid to a growing peptide chain ending with a D-amino acid. iii) C domain starter unit generally acylates the first amino acid with a β-hydroxy-carboxylic acid (typically a β-hydroxyl fatty acid).

iv) Heterocyclization (Cyc) domains catalyze both

peptide bond formation and subsequent cyclization of cysteine, serine or threonine residues. v) homologous Epimerization (E) domain flips the chirality of the last amino acid in the growing peptide. According to Raush[114], there also exists a Dual E/C domains which catalyze both epimerization and condensation reactions.

Figure___: Module and domain structure of NRPS: Complete NRPS consisting of three modules viz, initiation, elongation and termination. Condensation domain (C) showing approximate positions of the seven motifs. Other principal and ancillary domains such as Adenylation domain (A domain), N-Meth: N-methylation domain (optional – does not appear in all NRPS), PCP: Thiolation domain (T domain or Peptidyl Carrier Protein domain), Epi: Epimerization domain (optional). Other optional domains are: Heterocyclization, Oxidation, Reduction and Formylation domain (modified from Rausch[114])

_____________________________________________________Introduction______ Thioesterase domain (TE): The TE domain is about 250 amino acid residue located to the C-terminal end which is primarily involved in the addition of the last amino acid to the linear growing peptide chain. This domain has been found in the same location in the bacteria and fungi for the synthesis of tripeptide, bacitracin, enterobactin, gramicidin, pyoverdine, surfactin and tyrocidine[96]. In cyanobacteria, it is also involved in the formation of Anabaenapeptolide[15,16], Microcystin[16,21-23], Barbamide[17], Curacin[18], Nostopeptilide [24], Nostocyclopeptide[25]. Due to its strategic location, it can be said that the TE domain might involved in hydrolytic cleavage of the linear peptide product, i.e., termination of nonribosomal peptide biosynthesis. The TE domain generally has a core motif of GxSxG which is also found in acyltransferase domain of polyketide synthase.

A recent

mutation study of the conserved serine residue of the signature sequence (GxSxG) to alanine and deletion study of the entire TE domain of ACVsynthetase of Penicillium chrysogenum to analyze the role of TE domain in nonribosomal peptide synthetases revealed that there is drastic reduction in the product formation in both cases which clearly underlines the importance of TE domain[115].

Gene products of TE domains are about 220-340 amino acid

residue in length and show great homology to the TE domain involved in the fatty acid biosynthesis of the mammalian cells. Thus it can be inferred that TE domain plays an important role in the biosynthesis of peptides in the nonribosomal peptide synthetases system.

Other modifying domains: Nonribosomal peptide synthetases can also carry out an array of modification reactions N-acylation, N-methylation and epimerization.

These modifying

_____________________________________________________Introduction______ domains in the nonribosomal peptide synthetases dramatically increase the versatility and biological activity of nonribosomally synthesized peptides[2].

A)

Epimerization domains:

Epimerization domains generally resembles that of condensation domains but they have slightly different signature sequence[89].

Their main function is to

epimerize aminoacyl and peptidyl intermediates at the thioester stage and this reaction is reversible thus they can maintain a state of equilibrium between these two isomers.

B) Formyl transferase domain: This formylatiaon domain was first identified by Rouhiainen [15] in the anabaenopeptilide biosynthetic gene cluster.

The N-terminal region shows

homology to the co-substrate formyl tetrahydrofolate-dependent methionyl-tRNA formyltransferase.

They generally shows similirities to condensation domains

and they are usually linked to the first A domain.

C) N-methylation domain: The N-methyl transferase domain is involved in the N-methylated peptide bond formation of the primed amino acid. This was first found in the fungal system enniatin synthetase gene[116].

Generally N-met transferase genes are

integrated with the A domain between the core motif A8-A9. this domain is about 450 amino acid long and it shares sequence similarities to the S-adenosyl-Lmethionine (SAM)-dependent methyltransferease.

Because of its insertion

between A8-A9, N-methylation function can be gained or lose by domain insertion or deletion[117].

_____________________________________________________Introduction______

D) Oxidation domain: These domains are generally 200 amino acid residue showing sequence homolog to the DNA binding proteins. They are generally present in adenylation domains between the core motif A8-A9.

these domains are found in

epothilone[118] (EpoB), myxothiazol[119] (MtaC & MtaD).

In epothilone

biosynthesis, this domain is involve in the oxidation of methylthiozolinyl to methylthiazolcarboxy intermediate[120]. In case of barbamide biosynthesis gene cluster, no oxidation domain is found in A-domain of BarG, but it has been speculated

that

BarI

and

BarJ

has

been

involved

in

the

oxidative

decarboxylation[17].

E) Reduction domain: The reduction domain is about 400 amino acid long showing significant similarity to the nucleoside-diphosphate-sugar epimerase, flavonol reductase and NADPH dependent enzymes.

In nostocyclopeptide, the final peptidyl intermediate is

reduced to the linear aldehyde cyclization to form a stable imine bond[25].

Substrate specificity of NRPS: NRPS systems shows a moderately relaxed substrate specificity so as to allow incorporation of more than one amino acid which is greatly responsible for the formation

of

various

biosynthesis[96].

final

products

in

vivo

(for

example,

tyrocidine

However, some positions of a particular peptide are

significantly more resistant to replacement than others, reflecting the importance of the residues in these positions for the function of the product. The A domain was

shown

to

play

an

important

role

in

selecting

the

amino

acid

_____________________________________________________Introduction______ substrate[105,107]. A deep insight into the substrate binding was revealed when the structure of the A domain of gramicidin S synthetase 1 (GrsA), complexed with phenylalanine and adenosine monophosphate (AMP), was determined by crystallization[121].

By comparing the sequence of the phenylalanine-binding

pocket with the adenylation domain sequences in the databases, Stachelhaus [105] presented the selectivity-conferring code (or specificity code) of 10 amino acids for adenylation domains. He also provided general rules for inferring the substrate specificity tested these rules by mutations[105,113] using information on the crystal structure of GrsA to develop a computer method for finding specificity codes from the amino acid sequences of adenylation domains. Chang et al.[17] showed that the activity assay of adenylation domains of barD, barE

and barG for module 2 in an amino acid-dependent ATP-pyrophosphate exchange experiment supports the conclusion that barbamide is synthesized from acetate, L-phenylalanine, L-cysteine and L-leucine with trichloroleucine as a direct precursor by a mixed polyketide synthase/non-ribosomal polypeptide synthetase, thus confirming the moderately relaxed substrate specificity.

Colinearity between peptide synthetase and their products: Generally, in NRPS gene clusters the order of the coded activities is colinear with the structure of the product, and the number of modules is the same as the number of residues in the finished peptide [96,122]. Consequently, it is possible by analysing the sequence of the NRPS genes to determine the composition of the peptide, provided the substrate specificities of the adenylation domains are known. In may cases, which amino acid is activated by an adenylation domain can be deduced from the gene sequence. This is made possible by comparing

_____________________________________________________Introduction______ the so-called selectivity-conferring code of the adenylation domain with the known precedents, as described by [105,123]. The reverse is also valid: based on structural information the genes of a particular synthetase can be identified from a strain that produces more than one nonribosomal peptide. Currently, several nonlinear NRPSs are known, including the synthetases of syringomycin [124]), yersiniabactin [125], mycobactin [126] and bleomycin [127]. Some peptides are assembled by the iterative use of modules or domains, so that the peptide chain is composed of smaller repeated units. Examples of this type are the synthetases of enterobactin from Escherichia coli [128] and of gramicidin S from Brevibacillus brevis [129]. The activities and number of modules correspond only to a single set of the repetitive structure of the product

Modular structure of polyketide synthase (PKS):

Fig___: Core set of elongation domain showing Apo proteins (OH group attached) which are unable to participate in chain elongation. Apo proteins are post-translationally modified with pohsphopentathein arm in presence of PPTase for priming and are ready for chain elongation. (taken from Keating & Walsh [130] )

Polyketides (PKS) are large multifunctional protein complexes which catalyze the gradual condensation of simple building blocks.

Essentially, PKS are large

modular organization and each module carries all essential information for the recognition, activation and modification of one substrate in the form of COA thioester derivative of carboxylic acid into the growing chain. The number of

_____________________________________________________Introduction______ modules and their domain organization have a tight control over the final product[131]. There are three major classes of PKS systems classified on the basis of their synthesis and structural type of product. Type I PKS in bacteria are multienzyme complexes organized into linear modules and each module is responsible for a single specific chain elongation process and posttranstional modification of resulting compound.

Core PKS domains: Natural product biosynthesis by type I PKS proceeds in a linear stepwise fashion which begins with a loading unit. Component domains of polyketides consist of acyl-transferases (AT) for the loading of starter, extender and intermediate acyl units; acyl carrier proteins (ACP) which hold the growing macrolide as a thiol ester; b-keto-acyl synthases (KS) which catalyse chain extension; b-keto reductases (KR) responsible for the first reduction to an alochol functionality; dehydratases (DH)which eliminate water to give an unsaturated thiolester; enoyl reductases (ER) which catalyse the final reduction to full saturation; and finally a thiolesterase (TE) to catalyse macrolide release and cyclisation.

For

identification of the gene clusters involved in the biosynthesis of various cyanobacterial secondary metabolites molecular approaches have been used by several workers to elucidate the operon organization. For example, lyngbyatoxin, curacin A, jamaicamides and barbamide from Lyngbya majuscule [17-20], microcystin

from

Microcystis

aeruginosa

[22,23,86,108,132-134],

anabaenopeptilide from Anabaena flos-aquae [15].

Neilan et al. showed the

presence of type I PKS domains in several cyanobacteria[135,136]. A genetic PCR-based screening technique was used to screen the presence of PKS KSdomain in large number of laboratory and environmental samples. Analysis of the results shows presence of KS domain which uses acyl-COA as a starter unit.

_____________________________________________________Introduction______ Subsequently, in another study Ehrenreich et al. [83], in a combined NRPS-PKS study reported presence of NRPS A-domain and PKS KS domain in 20 marine and freshwater cyanobacteria.

Minimally, synthesis of polyketides requires three PKS domains.

The acyl

transferease (AT-domain) is responsible for the selection of substrate and is generally similar to that of A domain of NRPS. The substrate is generally malonyl coenzyme A thioesterase. This primed COA-thioester moiety is then transferred to the adjacent acyl carrier protein (ACP domain). These ACP’s are the second essential domains of PKS and are analogous to the PCP domain of the NRPS and works as a transport unit. The condensation step is similar to that of Claisen condensation which is catalyzed by the KS-domain. Thus, it can be said that the KS domain is similar to that of Condensation (C) domain of NRPS (Fig__:). To enumerate the exact reaction mechanism, Schwarzer & Marahiel[1] gave the exact sequence of reactions going on after the COA-thioester moiety has been primed.

Fig___: Reaction catalyzed by NRPS and PKS domains[1] First step in this reaction is the transfer of ketide chain to the active cystine residue of the KS-domain.

The primed (ACP-bound) malonate is further

decarboxylated, releasing a free nucleophile which is further condensed with the ketide chain.

This reaction produced β-keto carboxy acid which is further

gradually reduced by the auxiliary domains to produce either an intermediate like β-hydroxy carboxy acid and α, β-unsaturated ketide or a fully reduced aliphatic

_____________________________________________________Introduction______ carboxy acid. These reactions are usually carried out by the ketoreductase (KR), dehydrogenase (DH) and enoylreductase (ER)-domains. These reactions need NADPH as a cofactor to catalyze these reactions.

The final release of the

polypeptide after completion of the elongation and reduction is catalyzed by the TE domain[137].

_____________________________________________________Introduction______

References: 1 2 3 4 5 6

7 8

9 10

11 12 13

14 15 16 17

18

19

20 21

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