Academic conferences are a central part of our scientific world; however, the ongoing COVID-19 pandemic has made the organization of such events much more complex and difficult to plan. This is also true for the “6th Meeting on Regulating with RNA in Bacteria and Archaea,” an international, biannual conference, which was initially scheduled to take place in September of 2020 in St. Petersburg (Florida, USA). Instead, due to the pandemic, we converted our meeting to an online conference, which we are now looking forward to. Despite this delay in planning and the logistical complications that come with postponing conferences, the situation also prompted us to take a closer look at the developments in the field of microbial RNA biology and made us realize the tremendous progress we have made in the past few years. This is when the idea for this special issue was born.

The special issue contains a total of 15 articles, including 11 original research articles, three reviews, and one commentary. The topics included broadly cover the field of post-transcriptional gene regulation in bacteria with articles focusing on various current challenges in the field such as the discovery and annotation of regulatory RNAs, the role of RNA-binding proteins, RNA evolution, and the physiological consequences associated with RNA-based gene regulatory processes. Several of the featured articles also cover two of these aspects, or shed new light on previously investigated topics.

In general, the field of microbiology has been changing at previously unknown speeds. Full bacterial and archaeal genome sequences are now available in high numbers and at very low costs allowing microbiologists to address the physiological changes of whole organisms, rather than working on a “gene-by-gene” basis. Working with hundreds or thousands of genomes not only provides useful information on conserved microbial functions, it also exposes a vast abundance of unknown regulatory elements. These unknown regulators are frequently non-coding sequences in bacterial genomes and often involve regulatory RNA elements. Nevertheless, identifying and annotating these non-coding regulators is typically not easy, especially for non-model organisms. As pointed out in the review article by Stiens et al., the functional characterization of non-coding RNAs in mycobacteria has been lagging behind other organisms, which has complicated the research on these regulators in various organisms, including the major human pathogen Mycobacterium tuberculosis (Stiens et al., 2021).

Genome-wide expression analysis of total RNA or co-immunoprecipitation experiments of RNA-binding proteins have now exposed RNA regulators in almost all genomic regions of bacterial and archaeal chromosomes. Specifically, the 5′ and 3′ untranslated regions (UTRs) of coding sequences have been shown to carry high numbers of small regulatory RNAs (sRNAs), riboswitches, RNA-thermometers, and termination regulators; the large majority of which await characterization of their biological functions. Indeed, Desgranges et al. discovered that RsaG sRNA from Staphylococcus aureus is expressed from the 3’UTR of the uhpT gene (encoding a glucose-6-phosphate (G6P) transporter) and controls redox homeostasis in response changing environmental conditions (Desgranges et al., 2021). Interestingly, the rsaG sequence seems to evolve rapidly, indicating that the sRNA could be involved in the adaptation to other niches in related bacteria. Likewise, as revealed in the article by Svensson and Sharma, the CJnc190 sRNA of Campylobacter jejuni and the RepG sRNA of Helicobacter pylori are similar in sequence and their mechanisms of target regulation, yet the two sRNAs display different modes of biogenesis (Svensson & Sharma, 2021). While it is not fully understood if the two sRNA arose from the same ancestor, investigating their phylogenetic relation might be a valuable approach to better understand the evolution of regulatory RNAs outside the typical model organisms such as Escherichia coli.

This special issue covers several additional topics concentrating on bacteria that yet lack detailed studies regarding their non-coding RNA repertoire. For example, Lee et al. study the role of transcription antitermination for antibiotic resistance in Streptomyces coelicolor and through conservation analyses find that a similar mode of regulation is likely to be present in several related bacteria, as well as M. tuberculosis (Lee et al., 2021). The article by Prezza et al. take a bioinformatics approach on the RNA biology of Bacteroides species, which are important members of our intestinal microbiota (Prezza et al., 2021). The work predicts several uncharacterized sRNAs and RNA-binding proteins and thus provides an important resource for future studies focusing on RNA-based gene regulation in this genus and maybe other members of the human gut microbiome. This could also include bacterial pathogens that thrive in the human gut, such as Clostridioides difficile. C. difficile and various related bacteria produce a set of RNA-binding proteins that carry KH domain and might function as RNA chaperones. The review article by Olejniczak et al. focuses on this class of proteins and their putative physiological roles in various bacteria (Olejniczak et al., 2021).

In contrast to these new types of RNA-binding proteins, Hfq and CsrA are well-known to interact with RNA and are key contributors to RNA-based gene regulation in many microorganisms. Although these proteins have been studied for many years, new regulatory functions are still being discovered. Specifically, Sudo et al. reveal that Hfq controls virulence gene expression in enterohemorrhagic E. coli (EHEC) species by inhibiting the expression of the grlA and ler transcripts and that this process can occur in the absence of sRNA regulators (Sudo et al., 2021). In contrast, Lai et al. show that Hfq and Hfq-binding sRNAs can “get support” from other RNA-binding proteins such as CsrA, which binds to the Hfq-dependent Spot 42 sRNA and protects it from degradation by the major endoribonuclease, RNase E (Lai et al., 2021). This article is further accompanied by a Microcommentary by Stenum and Holmqvist (Stenum & Holmqvist, 2021). In addition, the review article by Richards and Belasco highlights the role of RNA structure, especially in in connection with riboswitch elements, on transcript stability and mRNA translation (Richards & Belasco, 2021).

RNase E together with Hfq and other proteins such as PNPase form a multi-protein complex, called the RNA degradosome. The degradosome has a major impact on RNA turn-over in many bacteria, yet, due to its size, studies of the complete degradosome have been challenging. The article by Dendooven et al. addresses problem using a combination of X-ray solution scattering, cryo-EM single particle analysis, and cryo-electron tomography to obtain a comprehensive view on this dynamic protein complex and how its structure is affected by the interaction with RNA (Dendooven et al., 2021). Interestingly, McQuail et al. discovered that in nitrogen-starved E. coli cells, Hfq and RNase E co-localize in so-called H-bodies that also include additional members of the degradosome, for example, PNPase and the helicase RhlB (McQuail et al., 2021). These results could provide important information on how bacteria manage their global RNA metabolism under conditions of stress and/or starvation. Another protein that might play into this process is RelA, which is part of the stringent response pathway. In addition to its role in synthesizing the second messenger (p)ppGpp in response to uncharged tRNA molecules, Basu et al. now show that RelA also interacts with RNA (Basu & Altuvia, 2021). The protein preferentially binds GGAG motifs present in the Shine-Dalgarno sequences of mRNAs and seems to also promote gene regulation by Hfq-dependent sRNAs.

The regulatory role of one specific Hfq-dependent regulator, that is GcvB sRNA, was investigated by Miyakoshi et al. GcvB has been studied in great detail in E. coli and Salmonella enterica and controls dozens of target mRNAs in both organisms, yet, the exact number of targets remained unknown. The authors took advantage of available large datasets and validated additional 21 targets of GcvB raising the total number of targets >50, which is currently the largest number of targets known for any Hfq-binding sRNA (Miyakoshi et al., 2021).

Finally, accumulating evidence suggests that proteins that we have previously associated with distinct post-transcriptional regulatory mechanisms might well also become involved in other RNA-centerd pathways. In fact, the work by Mohanty et al. indicates that RNase P, which is involved in the maturation of tRNAs in nearly all organisms, also affects the cellular RNA metabolism. These effects are distinct from other major ribonucleases, such RNase E and RNase III (Mohanty & Kushner, 2021), and could indicate that RNase P has yet undiscovered regulatory functions in bacteria and maybe higher organisms.

In summary, the microbial RNA field is in full swing and these are particularly interesting times for microbiologists studying RNA-based regulatory mechanisms in microorganisms. We hope that this special issue and the upcoming conference on “Regulating with RNA in Bacteria and Archaea” will allow us to explore more of this fascinating research and stimulate discussions among the scientists involved. Furthermore, we hope to inspire new researchers as well as young scientists to join the field and study the exciting world of microbial RNAs and RNA-binding proteins.

学术会议是我们科学世界的核心部分；然而，持续的 COVID-19 大流行使此类活动的组织变得更加复杂和难以计划。原定于 2020 年 9 月在圣彼得堡（美国佛罗里达州）举行的“第 6 次细菌和古生菌中 RNA 调控会议”也是如此，这是一个一年两次的国际会议。相反，由于大流行，我们将会议转换为在线会议，这是我们现在所期待的。尽管计划延迟以及会议推迟带来的后勤问题，但这种情况也促使我们仔细研究微生物 RNA 生物学领域的发展，并让我们意识到我们在过去几年中取得的巨大进步.

特刊共收录15篇文章，其中原创研究文章11篇，综述3篇，评论1篇。主题广泛涵盖细菌转录后基因调控领域，文章重点关注该领域当前面临的各种挑战，例如调控 RNA 的发现和注释、RNA 结合蛋白的作用、RNA 进化和生理后果与基于 RNA 的基因调控过程有关。几篇专题文章也涵盖了其中两个方面，或者对先前研究的主题提供了新的启示。

总的来说，微生物学领域一直在以前所未有的速度发生变化。完整的细菌和古细菌基因组序列现在大量可用且成本非常低，使微生物学家能够解决整个生物体的生理变化，而不是在“逐个基因”的基础上工作。使用数百或数千个基因组不仅可以提供有关保守微生物功能的有用信息，还可以揭示大量未知的调控元件。这些未知的调节因子通常是细菌基因组中的非编码序列，并且通常涉及调节 RNA 元件。然而，识别和注释这些非编码调节剂通常并不容易，尤其是对于非模式生物。正如 Stiens 等人在评论文章中指出的那样，结核分枝杆菌（Stiens 等人，  2021）。

总 RNA 的全基因组表达分析或 RNA 结合蛋白的免疫共沉淀实验现在已经在细菌和古细菌染色体的几乎所有基因组区域中暴露了 RNA 调节剂。具体来说，编码序列的 5' 和 3' 非翻译区 (UTR) 已被证明携带大量的小调节 RNA (sRNA)、核糖开关、RNA 温度计和终止调节剂。其中绝大多数等待其生物学功能的表征。事实上，Desgranges 等人。发现来自金黄色葡萄球菌的 RsaG sRNA 从uhpT基因的 3'UTR表达（编码葡萄糖 6-磷酸 (G6P) 转运蛋白）并控制氧化还原稳态以响应不断变化的环境条件（Desgranges 等，  2021）。有趣的是，rsaG序列似乎进化迅速，表明 sRNA 可能参与了对相关细菌其他生态位的适应。同样，正如 Svensson 和 Sharma 的文章所揭示的，空肠弯曲杆菌的 CJnc190 sRNA 和幽门螺杆菌的 RepG sRNA在序列和靶标调控机制上相似，但两种 sRNA 显示出不同的生物发生模式（Svensson 和 Sharma，  2021 年）。虽然目前尚不完全清楚这两个 sRNA 是否来自同一个祖先，但研究它们的系统发育关系可能是一种有价值的方法，可以更好地了解在大肠杆菌等典型模式生物之外调控 RNA 的进化。

本期特刊涵盖了几个其他主题，这些主题集中在细菌上，但缺乏对其非编码 RNA 库的详细研究。例如，李等人。研究转录抗终止在天蓝色链霉菌中对抗生素抗性的作用，并通过保护分析发现，在几种相关细菌以及结核分枝杆菌中可能存在类似的调节模式（Lee 等人，  2021 年）。Prezza 等人的文章。对拟杆菌属物种的 RNA 生物学采取生物信息学方法，拟杆菌属物种是我们肠道微生物群的重要成员（Prezza 等人，  2021）。这项工作预测了几种未表征的 sRNA 和 RNA 结合蛋白，因此为未来的研究提供了重要资源，该研究侧重于该属以及人类肠道微生物组的其他成员中基于 RNA 的基因调控。这也可能包括在人类肠道中茁壮成长的细菌病原体，例如艰难梭菌。C. difficile 和各种相关细菌产生一组 RNA 结合蛋白，这些蛋白携带 KH 结构域并可能作为 RNA 伴侣发挥作用。Olejniczak 等人的评论文章。专注于这类蛋白质及其在各种细菌中的假定生理作用（Olejniczak 等人，  2021 年）。

与这些新型 RNA 结合蛋白相比，众所周知，Hfq 和 CsrA 与 RNA 相互作用，并且是许多微生物中基于 RNA 的基因调控的关键因素。尽管这些蛋白质已经研究了很多年，但新的调节功能仍在被发现。具体来说，须藤等人。揭示 Hfq通过抑制grlA和ler转录物的表达来控制肠出血性大肠杆菌(EHEC) 物种中的毒力基因表达，并且该过程可以在没有 sRNA 调节剂的情况下发生（Sudo 等人，  2021）。相比之下，赖等人。表明 Hfq 和 Hfq 结合 sRNA 可以从其他 RNA 结合蛋白（如 CsrA）“获得支持”，CsrA 与 Hfq 依赖性 Spot 42 sRNA 结合并保护其免受主要内切核糖核酸酶 RNase E 的降解（Lai et al. ,  2021 年)。本文还附有 Stenum 和 Holmqvist 的微评论（Stenum 和 Holmqvist，  2021 年）。此外，Richards 和 Belasco 的评论文章强调了 RNA 结构在转录稳定性和 mRNA 翻译中的作用，特别是与核糖开关元件有关的作用（Richards & Belasco，  2021 年）。

RNase E 与 Hfq 和其他蛋白质（如 PNPase）一起形成多蛋白质复合物，称为 RNA 降解体。降解体对许多细菌的 RNA 转换具有重大影响，但由于其大小，对完整降解体的研究一直具有挑战性。Dendooven 等人的文章。结合使用 X 射线溶液散射、冷冻电镜单粒子分析和冷冻电子断层扫描来解决问题，以全面了解这种动态蛋白质复合物及其结构如何受到与 RNA 相互作用的影响（Dendooven 等人。 ,  2021 年)。有趣的是，McQuail 等人。发现在缺氮的大肠杆菌中细胞、Hfq 和 RNase E 共定位于所谓的 H 体中，这些 H 体还包括降解体的其他成员，例如 PNPase 和解旋酶 RhlB（McQuail 等人，  2021 年）。这些结果可以提供有关细菌如何在压力和/或饥饿条件下管理其全球 RNA 代谢的重要信息。另一种可能参与这一过程的蛋白质是 RelA，它是严格反应途径的一部分。除了在合成第二信使 (p)ppGpp 以响应不带电荷的 tRNA 分子中的作用外，Basu 等人。现在表明 RelA 也与 RNA 相互作用 (Basu & Altuvia,  2021 )。该蛋白质优先结合存在于 mRNA 的 Shine-Dalgarno 序列中的 GGAG 基序，并且似乎还促进了 Hfq 依赖性 sRNA 的基因调控。

Miyakoshi 等人研究了一种特定的 Hfq 依赖性调节剂 GcvB sRNA 的调节作用。GcvB 已在大肠杆菌和肠沙门氏菌中进行了非常详细的研究，并控制了这两种生物体中的数十种靶 mRNA，但靶标的确切数量仍然未知。作者利用可用的大型数据集并验证了额外的 21 个 GcvB 目标，使目标总数 > 50，这是目前已知的任何 Hfq 结合 sRNA 的最大目标数量（Miyakoshi 等人，  2021 年）。

最后，越来越多的证据表明，我们之前与不同的转录后调控机制相关的蛋白质也很可能参与其他以 RNA 为中心的途径。事实上，Mohanty 等人的工作。表明参与几乎所有生物体中 tRNA 成熟的 RNase P 也影响细胞 RNA 代谢。这些作用不同于其他主要的核糖核酸酶，例如 RNase E 和 RNase III (Mohanty & Kushner,  2021 )，并且可能表明 RNase P 在细菌和高等生物中尚未发现调节功能。

总之，微生物 RNA 领域如火如荼，对于微生物学家研究微生物中基于 RNA 的调控机制来说，这是特别有趣的时期。我们希望本期特刊和即将召开的“用 RNA 在细菌和古细菌中进行调控”会议能够让我们探索更多这项引人入胜的研究，并激发相关科学家之间的讨论。此外，我们希望激发新的研究人员和年轻科学家加入该领域并研究令人兴奋的微生物 RNA 和 RNA 结合蛋白世界。