Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin

Phylogenomic analyses of the genus Actinoplanes: description of four novel genera

The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade's distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.

Complete Genome Sequence of Actinoplanes sp. Strain L3-i22, Isolated from Soil in Japan

Here, we described the closed complete genome sequence of Actinoplanes sp. strain L3-i22, which was obtained from the assembly with long reads and subsequent polishing with short reads. The complete genome consists of a 12,014,766-bp chromosome, with a GC content of 71.4%, and contains no plasmids.

Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil

A novel protease-producing actinobacterium, designated strain NEAU-A11^T, was isolated from soil collected from Aohan banner, Chifeng, Inner Mongolia Autonomous Region, China, and characterised using a polyphasic approach. The hydrolytic enzymes, such as proteases, played critical roles in destruction of fungi by degrading the protein linkages to disrupt integrity in the cell wall. This suggested that the isolate could be a good biocontrol candidate against pathogens to control fungal diseases. On the basis of 16S rRNA gene sequence analysis, strain NEAU-A11^T was indicated to belong to the genus Actinoplanes and was most closely related to Actinoplanes rectilineatus JCM 3194 ^T (98.9%). Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were arabinose, xylose and glucose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. The predominant menaquinones were MK-9(H₄), MK-9(H₆) and MK-9(H₈). The major fatty acids were C_18:0, C_16:0, C_18:1 ω9c, C_17:0 and C_15:0. Genome sequencing revealed a genome size of 10,742,096 bp, a G + C content of 70.5% and 9,514 protein-coding genes (CDS), including 102 genes coding for protease. Moreover, Genome analysis showed that strain NEAU-A11^T contained 255 glycoside hydrolases (GHs), 152 glycosyl transferases (GTs), 40 carbohydrate esterases (CEs), 26 polysaccharide lyases (PLs), and 12 auxiliary activities (AAs) genes. Genome mining analysis using antiSMASH 5.0 led to the identification of 20 putative gene clusters responsible for the production of diverse secondary metabolites. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with A. rectilineatus JCM 3194 ^T in the genus Actinoplanes. Whole-genome phylogeny showed strain NEAU-A11^T formed a stable phyletic line with Actinoplanes lutulentus DSM 45883 ^T (97.6%). However, whole-genome average nucleotide identity value between strain NEAU-A11^T and its reference strains A. rectilineatus JCM 3194 ^T and A. lutulentus DSM 45883 ^T were found to be 81.1% and 81.6%, respectively. The levels of digital DNA-DNA hybridization between them were 24.6% (22.2-27.0%) and 24.8% (22.5-27.3%), respectively. The values were well below the criteria for species delineation of 70% for dDDH and 95-96% for ANI, suggesting that the isolate differed genetically from its closely related type strain. The content of G + C in genomic DNA was 70.5%, within the range of 67-76%. In addition, evidences from phenotypic, chemotaxonomic and genotypic studies indicated that strain NEAU-A11^T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes aureus sp. nov. is proposed, with NEAU-A11^T (= CCTCC AA 2019063 ^T = JCM 33971 ^T) as the type strain.

Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with sporulation occurring within host cells. The molecular determinants controlling Frankia sporulation have not been yet described. In order to highlight, for the first time, the molecular players potentially involved in Frankia sporulation, we conducted (i) a comparison of protein contents between Frankia spores and hyphae and (ii) a comparative genomic analysis of Frankia proteomes with sporulating and non-sporulating Actinobacteria. Among the main results, glycogen-metabolism related proteins, as well as oxidative stress response and protease-like proteins were overdetected in hyphae, recalling lytic processes that allow Streptomyces cells to erect sporogenic hyphae. Several genes encoding transcriptional regulators, including GntR-like, appeared up-regulated in spores, as well as tyrosinase, suggesting their potential role in mature spore metabolism. Finally, our results highlighted new proteins potentially involved in Frankia sporulation, including a pyrophosphate-energized proton pump and YaaT, described as involved in the phosphorelay allowing sporulation in Bacillus subtilis, leading us to discuss the role of a phosphorelay in Frankia sporulation.

Regulation of Sporangium Formation by BldD in the Rare Actinomycete Actinoplanes missouriensis

The rare actinomycete Actinoplanes missouriensis forms sporangia, including hundreds of flagellated spores that start swimming as zoospores after their release. Under conditions suitable for vegetative growth, zoospores stop swimming and germinate. A comparative proteome analysis between zoospores and germinating cells identified 15 proteins that were produced in larger amounts in germinating cells. They include an orthologue of BldD (herein named AmBldD [BldD of A. missouriensis]), which is a transcriptional regulator involved in morphological development and secondary metabolism in Streptomyces AmBldD was detected in mycelia during vegetative growth but was barely detected in mycelia during the sporangium-forming phase, in spite of the constant transcription of AmbldD throughout growth. An AmbldD mutant started to form sporangia much earlier than the wild-type strain, and the resulting sporangia were morphologically abnormal. Recombinant AmBldD bound a palindromic sequence, the AmBldD box, located upstream from AmbldD 3',5'-Cyclic di-GMP significantly enhanced the in vitro DNA-binding ability of AmBldD. A chromatin immunoprecipitation-sequencing analysis and an in silico search for AmBldD boxes revealed that AmBldD bound 346 genomic loci that contained the 19-bp inverted repeat 5'-NN(G/A)TNACN(C/G)N(G/C)NGTNA(C/T)NN-3' as the consensus AmBldD-binding sequence. The transcriptional analysis of 27 selected AmBldD target gene candidates indicated that AmBldD should repress 12 of the 27 genes, including bldM, ssgB, whiD, ddbA, and wblA orthologues. These genes are involved in morphological development in Streptomyces coelicolor A3(2). Thus, AmBldD is a global transcriptional regulator that seems to repress the transcription of tens of genes during vegetative growth, some of which are likely to be required for sporangium formation.IMPORTANCE The rare actinomycete Actinoplanes missouriensis undergoes complex morphological differentiation, including sporangium formation. However, almost no molecular biological studies have been conducted on this bacterium. BldD is a key global regulator involved in the morphological development of streptomycetes. BldD orthologues are highly conserved among sporulating actinomycetes, but no BldD orthologues, except one in Saccharopolyspora erythraea, have been studied outside the streptomycetes. Here, it was revealed that the BldD orthologue AmBldD is essential for normal developmental processes in A. missouriensis The AmBldD regulon seems to be different from the BldD regulon in Streptomyces coelicolor A3(2), but they share four genes that are involved in morphological differentiation in S. coelicolor A3(2).

Actinoplanes Swims into the Molecular Age

The survival strategy of Actinoplanes is fascinating from an evolutionary perspective, combining a short motile phase in an otherwise nonmotile, filamentous life cycle and the somewhat paradoxical concept of spores-normally thought of as a resting stage-that swim. In the first paper to report a molecular genetic analysis of development in Actinoplanes, the authors identify a key regulator of the entry into development (Y. Mouri, K. Konishi, A. Fujita, T. Tezuka, Y. Ohnishi, J Bacteriol 199:e00840-16, 2017, https://doi.org/10.1128/JB.00840-16).

Genetic and Transcriptional Analyses of the Flagellar Gene Cluster in Actinoplanes missouriensis

Actinoplanes missouriensis, a Gram-positive and soil-inhabiting bacterium, is a member of the rare actinomycetes. The filamentous cells produce sporangia, which contain hundreds of flagellated spores that can swim rapidly for a short period of time until they find niches for germination. These swimming cells are called zoospores, and the mechanism of this unique temporal flagellation has not been elucidated. Here, we report all of the flagellar genes in the bacterial genome and their expected function and contribution for flagellar morphogenesis. We identified a large flagellar gene cluster composed of 33 genes that encode the majority of proteins essential for assembling the functional flagella of Gram-positive bacteria. One noted exception to the cluster was the location of the fliQ gene, which was separated from the cluster. We examined the involvement of four genes in flagellar biosynthesis by gene disruption, fliQ, fliC, fliK, and lytA Furthermore, we performed a transcriptional analysis of the flagellar genes using RNA samples prepared from A. missouriensis grown on a sporangium-producing agar medium for 1, 3, 6, and 40 days. We demonstrated that the transcription of the flagellar genes was activated in conjunction with sporangium formation. Eleven transcriptional start points of the flagellar genes were determined using the rapid amplification of cDNA 5' ends (RACE) procedure, which revealed the highly conserved promoter sequence CTCA(N15-17)GCCGAA. This result suggests that a sigma factor is responsible for the transcription of all flagellar genes and that the flagellar structure assembles simultaneously.

IMPORTANCE

The biology of a zoospore is very interesting from the viewpoint of morphogenesis, survival strategy, and evolution. Here, we analyzed flagellar genes in A. missouriensis, which produces sporangia containing hundreds of flagellated spores each. Zoospores released from the sporangia swim for a short time before germination occurs. We identified a large flagellar gene cluster and an orphan flagellar gene (fliQ). These findings indicate that the zoospore flagellar components are typical of Gram-positive bacteria. However, the transcriptional analysis revealed that all flagellar genes are transcribed simultaneously during sporangium formation, a pattern differing from the orderly, regulated expression of flagellar genes in other bacteria, such as Salmonella and Escherichia coli These results suggest a novel regulatory mechanism for flagellar formation in A. missouriensis.

Therapeutic cyclic lipopeptides mining from microbes: latest strides and hurdles

Infectious diseases impose serious public health burdens and often have devastating consequences. The cyclic lipopeptides elaborated by bacteria Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Serratia, Propionibacterium and fungus Fusarium are very crucial in restraining the pathogens. Composed of a peptide and a fatty acyl moiety these amphiphilic metabolites exhibit broad spectrum antimicrobial effects. Among the plethora of cyclic lipopeptides, only selective few have emerged as robust antibiotics. For their functional vigor, polymyxin, daptomycin, surfactin, iturin, fengysin, paenibacterin and pseudofactin have been integrated in mainstream healthcare. Daptomycin has been a significant part of antimicrobial arsenal since the past decade. As the magnitude of drug resistance rises in unprecedented manner, the urgency of prospecting novel cyclic lipopeptides is being perceived. Intense research has revealed the implication of these bioactive compounds stretching beyond antibacterial and antifungal. Anticancer, immunomodulatory, prosthetic parts disinfection and vaccine adjuvancy are some of the validated prospects. This review discusses the emerging applications, mechanisms governing the biological actions, role of genomics in refining structure and function, semi-synthetic analog discovery, novel strain isolation, setbacks etc. Though its beyond the scope of the current topic, for holistic purpose, the role of lipopeptides in bioremediation and crop biotechnology has been briefly outlined. This updated critique is expected to galvanize innovations and diversify therapeutic recruitment of microbial lipopeptides.

Development of cultivation strategies for friulimicin production in Actinoplanes friuliensis

Actinoplanes friuliensis is a rare actinomycete which produces the highly potent lipopeptide antibiotic friulimicin. This lipopeptide antibiotic is active against a broad range of multi-resistant gram-positive bacteria such as methicillin-resistant Enterococcus sp. and Staphylococcus aureus (MRE, MRSA) strains. Antibiotic biosynthesis and regulation in actinomycetes is very complex. In order to study the biosynthesis of these species and to develop efficient production processes, standardized cultivation conditions are a prerequisite. For this reason a chemically defined production medium for A. friuliensis was developed. With this chemically defined medium it was possible to analyze the influence of medium components on growth and antibiotic biosynthesis. These findings were used to develop process strategies for friulimicin production. The focus of the project presented here was to develop cultivation strategies which included fed-batch and continuous cultivation processes. In fed-batch processes, volumetric productivities for friulimicin of 1-2 mg/l h were achieved. In a perfusion process, a very simple cell retention system, which works via sedimentation of the mycelial cell pellets, was used. With this system, stable continuous cultivations with cell retention were dependent on the dilution rate. With a dilution rate of 0.05 h(-1), cell retention worked well and volumetric productivity of friulimicin was enhanced to 3-5 mg/l h. With a higher dilution rate of 0.1 h(-1), friulimicin production ceased because cell retention was not possible any longer with this simple cell retention system. In order to support process development, cultivation data were used to characterize metabolic fluxes in the developed friulimicin production processes.

Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid

Here we report the complete and finished genome sequence of Streptomyces glaucescens GLA.O (DSM 40922), a natural producer of the alpha-glucosidase inhibitor acarbose, which is used in the treatment of type-2 diabetes mellitus. The genome of S. glaucescens GLA.O consists of two replicons, the chromosome with a size of 7,453,200bp and a G+C content of 73.0% as well as a plasmid named pSglau1 with a size of 170,574bp and a G+C content of 69.06%.

Complete genome sequence of Corynebacterium casei LMG S-19264T (=DSM 44701T), isolated from a smear-ripened cheese

We report the complete genome sequence of Corynebacterium casei LMG S-19264(T) (=DSM 44701(T)) which was isolated from the surface of an Irish farmhouse smear-ripened cheese. The genome of C. casei LMG S-19264(T) consists of three replicons: the chromosome (3,113,488 bp, 55.69% G+C content), the plasmid pCASE1 (2461 bp, 56.77% G+C content) and the plasmid pCASE2 (16,264 bp, 55.08% G+C content), encoding a total of 2908 protein coding genes. Analysis of the sequence data revealed a large region of ∼ 98 kb with an average G+C content of ∼ 65% that was acquired by horizontal gene transfer.

Complete genome sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer

We report the complete genome sequence of Corynebacterium vitaeruminis DSM 20294(T) which was identified as the producer of B vitamins in the rumen of cows. The genome of C. vitaeruminis DSM 20294(T) consists of a single replicon, the chromosome with a size of 2,931,780 bp and a G+C content of 65.53%. The genome encodes for 2,580 protein coding genes, among them those for a complete pathway to synthesize biotin.