The cellulolytic system of Streptomyces reticuli

Construction of a genome-editing system for the thermophilic actinomycete Streptomyces thermodiastaticus K5 strain

Thermophilic actinomycetes significantly contribute to the terrestrial carbon cycle via the rapid degradation of lignocellulosic polysaccharides in composts. In this study, a genome-editing system was constructed for the thermophilic actinomycete Streptomyces thermodiastaticus K5 strain, which was isolated from compost. The genome-editing plasmid (pGEK5) harboring nickase Cas9 was derived from the high-copy plasmid pL99 and used for the K5 strain. It was found that pGEK5 could easily be lost from the transformed clone through cultivation on apramycin-free medium and spore formation, enabling its reuse for subsequent genome-editing cycles. With the aid of this plasmid, mutations were sequentially introduced to 2 uracil-DNA glycosylase genes (Udg1 and Udg2) and 1 β-glucosidase gene (Bgl1). Thus, the genome-editing system using pGEK5 enables us to start the functional modification of this thermophilic actinomycete, especially for improved conversion of lignocellulosic biomass.

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.

Weaving of bacterial cellulose by the Bcs secretion systems

Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.

Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species

A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.

Distinct Substrate Specificities and Electron-Donating Systems of Fungal Lytic Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are powerful enzymes that oxidatively cleave glycosidic bonds in polysaccharides. The ability of these copper enzymes to boost the degradation of lignocellulose has greatly stimulated research efforts and biocatalytic applications within the biorefinery field. Initially found as oxidizing recalcitrant substrates, such as chitin and cellulose, it is now clear that LPMOs cleave a broad range of oligo- and poly-saccharides and make use of various electron-donating systems. Herein, substrate specificities and electron-donating systems of fungal LPMOs are summarized. A closer look at LPMOs as part of the fungal enzyme machinery might provide insights into their role in fungal growth and plant-pathogen interactions to further stimulate the search for novel LPMO applications.

Evolution and Ecology of Actinobacteria and Their Bioenergy Applications

The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.

Enzymes From Rare Actinobacterial Strains

Actinobacteria constitute rich sources of novel biocatalysts and novel natural products for medical and industrial utilization. Although actinobacteria are potential source of economically important enzymes, the isolation and culturing are somewhat tough because of its extreme habitats. But now-a-days, the rate of discovery of novel compounds producing actinomycetes from soil, freshwater, and marine ecosystem has increased much through the developed culturing and genetic engineering techniques. Actinobacteria are well-known source of their bioactive compounds and they are the promising source of broad range of industrially important enzymes. The bacteria have the capability to degrade a range of pesticides, hydrocarbons, aromatic, and aliphatic compounds (Sambasiva Rao, Tripathy, Mahalaxmi, & Prakasham, 2012). Most of the enzymes are mainly derived from microorganisms because of their easy of growth, minimal nutritional requirements, and low-cost for downstream processing. The focus of this review is about the new, commercially useful enzymes from rare actinobacterial strains. Industrial requirements are now fulfilled by the novel actinobacterial enzymes which assist the effective production. Oxidative enzymes, lignocellulolytic enzymes, extremozymes, and clinically useful enzymes are often utilized in many industrial processes because of their ability to catalyze numerous reactions. Novel, extremophilic, oxidative, lignocellulolytic, and industrially important enzymes from rare Actinobacterial population are discussed in this chapter.

Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes

The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B₁₂, transport of methionine and vitamin B₁₂, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B₁₂ riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.

Actinomycetes: A Source of Lignocellulolytic Enzymes

Lignocellulose is the most abundant biomass on earth. Agricultural, forest, and agroindustrial activities generate tons of lignocellulosic wastes annually, which present readily procurable, economically affordable, and renewable feedstock for various lignocelluloses based applications. Lignocelluloses are the focus of present decade researchers globally, in an attempt to develop technologies based on natural biomass for reducing dependence on expensive and exhaustible substrates. Lignocellulolytic enzymes, that is, cellulases, hemicellulases, and lignolytic enzymes, play very important role in the processing of lignocelluloses which is prerequisite for their utilization in various processes. These enzymes are obtained from microorganisms distributed in both prokaryotic and eukaryotic domains including bacteria, fungi, and actinomycetes. Actinomycetes are an attractive microbial group for production of lignocellulose degrading enzymes. Various studies have evaluated the lignocellulose degrading ability of actinomycetes, which can be potentially implemented in the production of different value added products. This paper is an overview of the diversity of cellulolytic, hemicellulolytic, and lignolytic actinomycetes along with brief discussion of their hydrolytic enzyme systems involved in biomass modification.

Characterization and phylogenetic analysis of cellulase producing Streptomyces noboritoensis SPKC1

A cellulase producing strain of Actinomycetes was isolated from soil samples which were collected from Southwest ghats, Kerala, India at a depth of 6-12 inches and Actinomycetes was characterized by morphological, cultural, physiological, chemotaxonomical and phylogenetic analysis. The 16S rRNA region of this strain was amplified and sequenced. The Neighbor-joining and Maximum Parsimony algorithm with topology tree of 16S rRNA was constructed. Based on results of observation and phylogenetic analysis, the strain SPKC1 was proved to belong to the species Streptomyces noboritoensis with cellulase activity. The Carboxy Methyl Cellulose (CMCase) activities of the strain SPKC1 on eighth day an amount of 910 microg/ml of glucose, 210 microg/ml of protein and 850 mg/100 ml of growth (biomass) on ninth day were recorded. In exocellulase activity strain SPKC1 on first day an amount of 500 microg/ml glucose was produced.

Thermostable cellulases from Streptomycessp.: scale-up production in a 50-l fermenter

Thermostable cellulase was produced by Streptomyces sp. T3-1 grown in a 50-l fermenter. Maximum cellulase activity was attained on the fourth day when agitation speeds and aeration rates were controlled at 300 rpm and 0.75 vvm, respectively. Maximum enzyme activities were: 148 IU CMCase ml(-1), 45 IU Avicelase ml(-1), and 137 IU beta-glucosidase ml(-1) with productivity of 326 IU l(-1) h(-1), which were 10-32% higher than the values obtained in shake-flask cultures.

Chitin degradation by cellulolytic anaerobes and facultative aerobes from soils and sediments

Species of strictly and facultatively anaerobic cellulolytic bacteria from soils and sediments were examined for the ability to degrade chitin. Of 22 species studied, 16 degraded insoluble chitin. Cellulomonas uda, which was selected for a comparative study of its cellulase and chitinase enzyme systems, produced different enzyme systems for the degradation of cellulose and chitin and different patterns of regulation of production of the two enzyme systems were observed. Moreover, C. uda utilized chitin as a source of nitrogen for the degradation of cellulose. In natural environments, the ability to use chitin as a nitrogen source may confer on cellulolytic microorganisms, such as C. uda, a selective advantage over other cellulolytic microbes.

Primary metabolism and its control in streptomycetes: a most unusual group of bacteria

Streptomycetes are Gram-positive bacteria with a unique capacity for the production of a multitude of varied and complex secondary metabolites. They also have a complex life cycle including differentiation into at least three distinct cell types. Whilst much attention has been paid to the pathways and regulation of secondary metabolism, less has been paid to the pathways and the regulation of primary metabolism, which supplies the precursors. With the imminent completion of the total genome sequence of Streptomyces coelicolor A3(2), we need to understand the pathways of primary metabolism if we are to understand the role of newly discovered genes. This review is written as a contribution to supplying these wants. Streptomycetes inhabit soil, which, because of the high numbers of microbial competitors, is an oligotrophic environment. Soil nutrient levels reflect the fact that plant-derived material is the main nutrient input; i.e. it is carbon-rich and nitrogen- and phosphate-poor. Control of streptomycete primary metabolism reflects the nutrient availability. The variety and multiplicity of carbohydrate catabolic pathways reflects the variety and multiplicity of carbohydrates in the soil. This multiplicity of pathways has led to investment by streptomycetes in pathway-specific and global regulatory networks such as glucose repression. The mechanism of glucose repression is clearly different from that in other bacteria. Streptomycetes feed by secreting complexes of extracellular enzymes that break down plant cell walls to release nutrients. The induction of these enzyme complexes is often coordinated by inducers that bear no structural relation to the substrate or product of any particular enzyme in the complex; e.g. a product of xylan breakdown may induce cellulase production. Control of amino acid catabolism reflects the relative absence of nitrogen catabolites in soil. The cognate amino acid induces about half of the catabolic pathways and half are constitutive. There are reduced instances of global carbon and nitrogen catabolite control of amino acid catabolism, which again presumably reflects the relative rarity of the catabolites. There are few examples of feedback repression of amino acid biosynthesis. Again this is taken as a reflection of the oligotrophic nature of the streptomycete ecological niche. As amino acids are not present in the environment, streptomycetes have rarely invested in feedback repression. Exceptions to this generalization are the arginine and branched-chain amino acid pathways and some parts of the aromatic amino acid pathways which have regulatory systems similar to Escherichia coli and Bacillus subtilis and other copiotrophic bacteria.