Utilization of orange peel waste for sustainable amino acid production by Corynebacterium glutamicum

Oranges are the most processed fruit in the world-it is therefore apparent that the industrial production of orange juice generates large quantities of orange peel as a by-product. Unfortunately, the management of the orange peel waste leads to economic and environmental problems. Meanwhile, the use of sustainable raw materials for the production of bulk chemicals, such as amino acids, is becoming increasingly attractive. To address both issues, this study focused on the use of orange peel waste as a raw material for media preparation for the production of amino acids by engineered Corynebacterium glutamicum. C. glutamicum grew on pure orange peel hydrolysate (OPH) and growth was enhanced by the addition of a nitrogen source and a pH buffer. Inhibitory effects by the combination of high concentrations of OPH, (NH4)2SO4, and MOPS buffer in the wild-type strain (WT), were overcome in the tyrosine-producing engineered C. glutamicum strain AROM3. Genetic modifications that we identified to allow for improved growth rates under these conditions included the deletions of the vanillin dehydrogenase gene vdh, the ʟ-lactate dehydrogenase gene ldhA and the 19 genes comprising cluster cg2663-cg2686. A growth inhibiting compound present in high concentrations in the OPH is 5-(hydroxymethyl)furfural (HMF). We identified vdh as being primarily responsible for the oxidation of HMF to its acid 5-hydroxymethyl-2-furancarboxylic acid (HMFCA), as the formation of HMFCA was reduced by 97% upon deletion of vdh in C. glutamicum WT. In addition, we showed that growth limitations could be overcome by adjusting the media preparation, using a combination of cheap ammonia water and KOH for pH neutralization after acidic hydrolysis. Overall, we developed a sustainable medium based on orange peel waste for the cultivation of C. glutamicum and demonstrated the successful production of the exemplary amino acids ʟ-arginine, ʟ-lysine, ʟ-serine, ʟ-valine and ʟ-tyrosine.

CdbC: a disulfide bond isomerase involved in the refolding of mycoloyltransferases in Corynebacterium glutamicum cells exposed to oxidative conditions

In Corynebacterium glutamicum cells, cdbC, which encodes a protein containing the CysXXCys motif, is regulated by the global redox-responsive regulator OsnR. In this study, we assessed the role of the periplasmic protein CdbC in disulfide bond formation and its involvement in mycomembrane biosynthesis. Purified CdbC efficiently refolded scrambled RNaseA, exhibiting prominent disulfide bond isomerase activity. The transcription of cdbC was decreased in cells grown in the presence of the reductant dithiothreitol (DTT). Moreover, unlike wild-type and cdbC-deleted cells, cdbC-overexpressing (P180-cdbC) cells grown in the presence of DTT exhibited retarded growth, abnormal cell morphology, increased cell surface hydrophobicity and altered mycolic acid composition. P180-cdbC cells cultured in a reducing environment accumulated trehalose monocorynomycolate, indicating mycomembrane deformation. Similarly, a two-hybrid analysis demonstrated the interaction of CdbC with the mycoloyltransferases MytA and MytB. Collectively, our findings suggest that CdbC, a periplasmic disulfide bond isomerase, refolds misfolded MytA and MytB and thereby assists in mycomembrane biosynthesis in cells exposed to oxidative conditions.

Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance?

PURPOSE

Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation.

CONCLUSIONS

The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.

The cysS gene (ncgl0127) of Corynebacterium glutamicum is required for sulfur assimilation and affects oxidative stress-responsive cysteine import

The OsnR protein functions as a transcriptional repressor of genes involved in redox-dependent stress responses. Here, we studied Corynebacterium glutamicum ORF ncgl0127 (referred to as cysS in this study), one of the target genes of OsnR, to reveal its role in osnR-mediated stress responses. The ΔcysS strain was found to be a cysteine auxotroph, and the transcription levels of the sulfur assimilatory genes and cysR, the master regulatory gene for sulfur assimilation, were low in this strain. Complementation of the strain with cysR transformed the strain into a cysteine prototroph. Cells challenged with oxidants or cysteine showed transcriptional stimulation of the cysS gene and decreased transcription of the ncgl2463 gene, which encodes a cysteine/cystine importer. The transcription of the ncgl2463 gene was increased in the ΔcysS strain and further stimulated by cysteine. Unlike the wild-type strain, ΔcysS cells grown with an excess amount of cysteine showed an oxidant- and alkylating agent-resistant phenotype, suggesting deregulated cysteine import. Collectively, our data suggest that the cysS gene plays a positive role in sulfur assimilation and a negative role in cysteine import, in particular in cells under oxidative stress.

Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance

Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.

Genetic Determinants of Stress Resistance in Desiccated Salmonella enterica

Enteric pathogens, including Salmonella, are capable of long-term survival after desiccation and resist heat treatments that are lethal to hydrated cells. The mechanisms of dry-heat resistance differ from those of wet-heat resistance. To elucidate the mechanisms of dry-heat resistance in Salmonella, screening of the dry-heat resistance of 108 Salmonella strains, representing 39 serotypes, identified the 22 most resistant and the 8 most sensitive strains for comparative genome analysis. A total of 289 genes of the accessory genome were differently distributed between resistant and sensitive strains. Among these genes, 28 proteins with a putative relationship to stress resistance were selected for to quantify relative gene expression before and after desiccation and expression by solid-state cultures on agar plates relative to cultures growing in liquid culture media. Of these 28 genes, 15 genes were upregulated (P < 0.05) after desiccation or by solid-state cultures on agar plates. These 15 genes were cloned into the low-copy-number vector pRK767 under the control of the lacZ promoter. The expression of 6 of these 15 genes increased (P < 0.05) resistance to dry heat and to treatment with pressure of 500 MPa. Our finding extends the knowledge of mechanisms of stress resistance in desiccated Salmonella to improve control of this bacterium in dry food. IMPORTANCE This study directly targeted an increasing threat to food safety and developed knowledge and targeted strategies that can be used by the food industry to help reduce the risk of foodborne illness in their dry products and thereby reduce the overall burden of foodborne illness. Genomic and physiological analyses have elucidated mechanisms of bacterial resistance to many food preservation technologies, including heat, pressure, disinfection chemicals, and UV light; however, information on bacterial mechanisms of resistance to dry heat is scarce. Mechanisms of tolerance to desiccation likely also contribute to resistance to dry heat, but this assumption has not been verified experimentally. It remains unclear how mechanisms of resistance to wet heat relate to dry-heat resistance. Thus, this study will fill a knowledge gap to improve the safety of dry foods.

OsnR is an autoregulatory negative transcription factor controlling redox-dependent stress responses in Corynebacterium glutamicum

Background

Corynebacterium glutamicum is used in the industrial production of amino acids and nucleotides. During the course of fermentation, C. glutamicum cells face various stresses and employ multiple regulatory genes to cope with the oxidative stress. The osnR gene plays a negative regulatory role in redox-dependent oxidative-stress responses, but the underlying mechanism is not known yet.

Results

Overexpression of the osnR gene in C. glutamicum affected the expression of genes involved in the mycothiol metabolism. ChIP-seq analysis revealed that OsnR binds to the promoter region of multiple genes, including osnR and cg0026, which seems to function in the membrane-associated redox metabolism. Studies on the role of the osnR gene involving in vitro assays employing purified OsnR proteins and in vivo physiological analyses have identified that OsnR inhibits the transcription of its own gene. Further, oxidant diamide stimulates OsnR-binding to the promoter region of the osnR gene. The genes affected by the overexpression of osnR have been found to be under the control of σ^H. In the osnR-overexpressing strain, the transcription of sigH is significantly decreased and the stimulation of sigH transcription by external stress is lost, suggesting that osnR and sigH form an intimate regulatory network.

Conclusions

Our study suggests that OsnR not only functions as a transcriptional repressor of its own gene and of those involved in redox-dependent stress responses but also participates in the global transcriptional regulation by controlling the transcription of other master regulators, such as sigH.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01693-1.

Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals

Water stress decreases the health and quality of horticulture crops by inhibiting photosynthesis, transpiration, and nutrient uptake. Application of plant growth promoting rhizobacteria (PGPR) can increase the growth, stress tolerance, and overall quality of field and greenhouse grown crops subjected to water stress. Here, we evaluated Serratia plymuthica MBSA-MJ1 for its ability to increase plant growth and quality of Petunia × hybrida (petunia), Impatiens walleriana (impatiens), and Viola × wittrockiana (pansy) plants recovering from severe water stress. Plants were treated weekly with inoculum of MBSA-MJ1, and plant growth and quality were evaluated 2 weeks after recovery from water stress. Application of S. plymuthica MBSA-MJ1 increased the visual quality and shoot biomass of petunia and impatiens and increased the flower number of petunia after recovery from water stress. In addition, in vitro characterizations showed that MBSA-MJ1 is a motile bacterium with moderate levels of antibiotic resistance that can withstand osmotic stress. Further, comprehensive genomic analyses identified genes putatively involved in bacterial osmotic and oxidative stress responses and the synthesis of osmoprotectants and vitamins that could potentially be involved in increasing plant water stress tolerance. This work provides a better understanding of potential mechanisms involved in beneficial plant-microbe interactions under abiotic stress using a novel S. plymuthica strain as a model.

Thiol-specific oxidant diamide downregulates whiA gene of Corynebacterium glutamicum, thereby suppressing cell division and metabolism

The whiA (NCgl1527) gene from Corynebacterium glutamicum plays a crucial role during cell growth, and WhiA is recognized as the transcription factor for genes involved in cell division. In this study, we assessed the regulatory role of the gene in cell physiology. Transcription of the gene was specifically downregulated by the thiol-specific oxidant, diamide, and by heat stress. Cells exposed to diamide showed decreased transcription of genes involved in cell division and these effects were more profound in ΔwhiA cells. In addition, the ΔwhiA cells showed sensitivity to thiol-specific oxidants, DNA-damaging agents, and high temperature. Further, downregulation of sigH (NCgl0733), the central regulator in stress responses, along with master regulatory genes in cell metabolism, was observed in the ΔwhiA strain. Moreover, the amount of cAMP in the ΔwhiA cells in the early stationary phase was only at 30% level of that for the wild-type strain. Collectively, our data indicate that the role of whiA is to downregulate genes associated with cell division in response to heat or thiol-specific oxidative stress, and may suggest a role for the gene in downshifting cell metabolism by downregulating global regulatory genes when growth condition is not optimal for cells.

Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1

Deinococcus radiodurans is well known for its extreme resistance to ionizing radiation (IR). Since reactive oxygen species generated by IR can damage various cellular components, D. radiodurans has developed effective antioxidant systems to cope with this oxidative stress. dr1765 from D. radiodurans is predicted to encode an alkyl hydroperoxidase-like protein (AhpD family), which is implicated in the reduction of hydrogen peroxide (H₂O₂) and organic hydroperoxides. In this study, we constructed a dr1765 mutant strain (Δdr1765) and examined the survival rate after H₂O₂ treatment. Δdr1765 showed a significant decrease in the H₂O₂ resistance compared to the wild-type strain. We also determined the crystal structure of DR1765 at 2.27 Å resolution. DR1765 adopted an all alpha helix protein fold representative of the AhpD-like superfamily. Structural comparisons of DR1765 with its structural homologues revealed that DR1765 possesses the Glu74-Cys86-Tyr88-Cys89-His93 signature motif, which is conserved in the proton relay system of AhpD. Complementation of Δdr1765 with dr1765 encoding C86A or C89A mutation failed to restore the survival rate to wild-type level. Taken together, these results suggest that DR1765 might function as an AhpD to protect cells from oxidative stress.

Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture

During aerobic growth, the Gram-positive facultative anaerobe and opportunistic human pathogen Streptococcus pneumoniae generates large amounts of hydrogen peroxide that can accumulate to millimolar concentrations. The mechanism by which this catalase-negative bacterium can withstand endogenous hydrogen peroxide is incompletely understood. The enzyme alkylhydroperoxidase D (AhpD) has been shown to contribute to pneumococcal virulence and oxidative stress responses in vivo We demonstrate here that SpAhpD exhibits weak thiol-dependent peroxidase activity and, unlike the previously reported Mycobacterium tuberculosis AhpC/D system, SpAhpD does not mediate electron transfer to SpAhpC. A 2.3-Å resolution crystal structure revealed several unusual structural features, including a three-cysteine active site architecture that is buried in a deep pocket, in contrast to the two-cysteine active site found in other AhpD enzymes. All single-cysteine SpAhpD variants remained partially active, and LC-MS/MS analyses revealed that the third cysteine, Cys-163, formed disulfide bonds with either of two cysteines in the canonical Cys-78-X-X-Cys-81 motif. We observed that SpAhpD formed a dimeric quaternary structure both in the crystal and in solution, and that the highly conserved Asn-76 of the AhpD core motif is important for SpAhpD folding. In summary, SpAhpD is a weak peroxidase and does not transfer electrons to AhpC, and therefore does not fit existing models of bacterial AhpD antioxidant defense mechanisms. We propose that it is unlikely that SpAhpD removes peroxides either directly or via AhpC, and that SpAhpD cysteine oxidation may act as a redox switch or mediate electron transfer with other thiol proteins.