File Name: recombinant protein folding and misfolding in escherichia coli .zip
Scott A. Lesley, Jim Graziano, Charles Y. Cho, Mark W.
- Recombinant protein folding and misfolding in Escherichia coli
- Protein folding, misfolding, and refolding of therapeutic proteins
Recombinant protein folding and misfolding in Escherichia coli
Scott A. Lesley, Jim Graziano, Charles Y. Cho, Mark W. Knuth, Heath E. Proper protein folding is key to producing recombinant proteins for structure determination. We have examined the effect of misfolded recombinant protein on gene expression in Escherichia coli. Comparison of expression patterns indicates a unique set of genes responding to translational misfolding.
The response is in part analogous to heat shock and suggests a translational component to the regulation. We have further utilized the expression information to generate reporters responsive to protein misfolding. These reporters were used to identify properly folded recombinant proteins and to create soluble domains of insoluble proteins for structural studies.
Structural genomics efforts are an important element of evaluating gene function. Protein expression and purification are key processes in these studies, and are often limited by the ability to produce properly folded recombinant protein. Escherichia coli is a common expression host that often makes misfolded protein when obliged to overproduce non-native gene products.
It is easy to overlook that this workhorse is itself an evolved biological organism reacting to a stress, namely overproduction of a foreign gene product. Gene expression in response to protein misfolding is key to understanding the reaction to this stress and potential solutions to the practical aspects of recombinant protein expression. A variety of environmental stresses cause protein denaturation resulting in a classical heat-shock response.
Unfolded protein is the stimulus for the change in gene expression Parsell and Sauer, DnaK is also a central transcription-regulator by negatively influencing the transcription factor RpoH Liberek and Georgopoulos, ; McCarty et al.
DnaK—RpoH interaction provides a feedback mechanism and is the proposed switch by which the cell senses the level of unfolded protein and can respond through appropriate gene expression. A major source of unfolded proteins in vivo is the nascent chain of translating genes. Gene expression in response to translational stress is related to the heat-shock response Parsell and Sauer, , but has not been closely examined. Genome arrays used to study global gene expression in E. To study translational misfolding rather than heat stress, we used recombinant expression of folded and misfolded proteins as a stimulus.
Our results indicate a unique set of genes respond to translational misfolding. The nature of these genes implies that many known heat-shock and chaperone proteins, as well as ribosome-associated proteins suggestive of translational regulation, are induced to deal with translational stress.
We have applied these results in a practical way by developing a screen to improve our ability to generate recombinant proteins for structural studies.
Misfolded protein often appears as insoluble aggregates when overexpressed in E. Several recent approaches have been used to detect soluble recombinant protein.
They utilize protein fusion to a reporter gene such as CAT Maxwell et al. Though convenient, these reporters have the potential to be biased by the nature of the fusion. The reporter portion of the fusion may alter the solubility of the target protein, either positively or negatively, giving unexpected results when expressing in the absence of the reporter fusion.
By utilizing a sensory and regulatory system already existing in the host, we have created a general screen for detecting misfolded, and typically insoluble, recombinant proteins without the requirement of a direct protein fusion. We have also demonstrated the utility of this approach combined with mutagenesis to create soluble fragments of recombinant proteins in E. The approach provides a general means of providing folded domains for structural studies.
Clones expressing properly folded or misfolded human proteins were obtained from the GeneStorm collection Invitrogen. Thermotoga maritima genes were amplified from genomic DNA and cloned into the expression vector pMH1 which encodes a 12 amino acid N-terminal tag containing a 6X-histidine repeat for purification and detection.
Putative domains comprised of bases 1—, — and — were amplified from the full-length template and cloned into pMH1. The above template was also used in amplifications of the full-length gene for fragmentation. Two micrograms of the Rep68 amplifer were used in each of five fragmentation reactions containing 1, 0.
Each pool was used as above for blunt cloning and ligation into pMH1 as above and introduced into the reporter cell line HK 57 for screening. Thermotoga proteins used for expression studies evaluating proteins of known expression characteristics were cloned into pMH1 as described above.
Protein expression was induced by the addition of l -arabinose to a final concentration of 0. Fractionation of soluble and insoluble proteins was performed by centrifugation.
Cultures were resuspended in 50 mM Tris pH 7. Cell debris and insoluble protein aggregates were pelleted by centrifugation at g for 15 min. The soluble fraction was removed and the pellets resuspended in an equivalent volume of lysis buffer.
Labeled mRNA was prepared and hybridized to an E. This gene chip contains mer oligonucleotide probes for each of the known E. Standard Affymetrix GeneChip analysis software was used to measure individual gene expression and to perform pairwise comparison of gene expression levels for pre-induction and post-induction samples.
Comparisons of changes in gene expression for properly folded and misfolded genes were analyzed for individual gene probe sets. Cultures were induced with a final concentration of 0.
These antibiotics provide a convenient method of lysis in microplate format without the need to add detergents that might solublize misfolded protein. Cultures were harvested after 2 h total of induction by centrifugation at maximum speed for 15 min to pellet cell debris on the bottom of the wells. This calculation was found empirically to provide good distinction between soluble and insoluble proteins.
To examine gene expression as a result of misfolded protein, representative genes were cloned as fusion proteins to thioredoxin under control of the tightly regulated arabinose promoter. PLA is almost entirely soluble, as determined by cell lysis and fractionation by centrifugation Figure 1. Further evidence of proper folding of this protein was obtained through dynamic light scattering of purified protein and the ability to crystallize it from a single affinity purification step unpublished data.
Under equivalent expression conditions, LCK is expressed almost exclusively as insoluble protein. Both proteins were expressed at sufficient levels to be the predominant translation product. Recombinant protein expression within E. These genes, then, are likely responsive to misfolded protein in the cell and may play a role within E. The heat-shock transcription factor RpoH is normally repressed by interaction with the chaperone protein DnaK.
In the presence of misfolded protein, DnaK binds to that protein thereby allowing RpoH to stimulate transcription of heat-shock promoters Liberek and Georgopoulos, Upstream regions of many of the induced genes in Table I show the presence of RpoH-dependant promoter sequences. Further evidence of the important role played by RpoH is provided by expression profiling results performed from an rpo H mutant KY expressing misfolded LCK protein compared to a non-expressing control. A strikingly different expression profile is seen in the case of the rpo H mutant Tables I and II.
The majority of the genes induced by the misfolded protein in the wild-type strain are poorly induced in the rpo H mutant indicating that they are directly or indirectly under the control of this transcription factor. Not surprisingly, many of the genes induced by translational misfolding have known chaperone activity.
These include the well characterized dna J, dna K and grp E genes. The corresponding proteins interact as a complex with misfolded or denatured protein in an ATP-dependant repair process. Likewise, mop AB genes forming the GroELS folding repair complex are induced under translational misfolding conditions. IbpAB are small heat-shock polypeptides associated with inclusion body aggregates of recombinant protein Allen et al.
Whereas they do not appear to behave as folding chaperones directly, they bind misfolded protein and interact with the DnaJK GrpE proteins as a chaperone system Thomas and Baneyx, Hsp33, the gene product of the yrf I gene was recently identified as a chaperone protein responsive to oxidizing conditions Veinger et al. Genes implicated in degradation of denatured protein are also induced by translational misfolding.
The lon , clp BP and hsl UV protease genes are expressed at increased levels. Under normal cell growth these proteases serve an important recycling function. Insoluble aggregates are relatively resistant to proteolysis and this recycling pathway is ineffective for recombinant protein expression. Other heat-shock genes associated with the ribosome are induced under conditions of translational misfolding.
Heat shock also increases the level of Hspbinding implying increased dissociation of 50S and 30S subunits. Further suggestion of ribosomal dissociation comes from the induction of fts J rrm J.
This enzyme methylates 23S rRNA at position located within the peptidyl transferase center of the ribosome Caldas et al. Particularly striking in the rpo H mutant is the large increase in transcripts of the cold-shock proteins CSPs. These genes are not affected by heat shock 9 , but are associated with a transient halt of translation.
Increased expression of CSPs under conditions that reduce chaperone expression rpo H is an indication of paused translation. Taken together, these results suggest a translational regulatory response to misfolded protein. Such regulation might involve rRNA demethylation, as a consequence of translational misfolding.
This hypothesis is an interesting regulatory mechanism currently under investigation. In addition to these known heat-shock genes, yag U, yci S, ybe D, yej G and yhg I show increased expression. Most of these proteins are relatively small and generally acidic. One speculation is that some of these proteins perform a similar role to IbpAB in the direct recognition and sequestering of misfolded protein.
However, only IbpAB have been associated with misfolded and aggregated protein. Induction levels of ibp AB are much higher and these other proteins may be present at lower levels. Interestingly, knockout mutations of ibp AB have relatively little affect on cell growth and viability Thomas and Baneyx, ; data not shown suggesting some functional redundancy within the cell.
A more detailed characterization is shown below. The response observed, then, appears to be a general result of protein misfolding rather than a specific response to any particular protein. These reporters provide a simple means of identifying misfolded protein through a sensitive enzymatic assay and the ibp AB promoter fusion was chosen as the reporter for further studies. For identifying protein derivatives that have improved folding properties in a recombinant environment, we also developed an ELISA-like assay compatible with high-throughput screening instrumentation.
To evaluate soluble protein levels in a high-throughput system, non-denatured cell lysates must be prepared using conditions compatible with rapid screening in microplates.
Protein folding, misfolding, and refolding of therapeutic proteins
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Metrics details. Different species of microorganisms including yeasts, filamentous fungi and bacteria have been used in the past 25 years for the controlled production of foreign proteins of scientific, pharmacological or industrial interest. A major obstacle for protein production processes and a limit to overall success has been the abundance of misfolded polypeptides, which fail to reach their native conformation. The presence of misfolded or folding-reluctant protein species causes considerable stress in host cells. The characterization of such adverse conditions and the elicited cell responses have permitted to better understand the physiology and molecular biology of conformational stress.
CRM, which retains the same inflammatory and immune-stimulant properties as diphtheria toxin but with reduced toxicity, has been used as a safe carrier in conjugated vaccines. Expression of recombinant CRM in E. Soluble expression attempts in Bacillus subtilis , P. Multiple approaches have been attempted to produce CRM in E. Recently, alternative methods for recovery of insoluble proteins expressed in E.
Substantial progress has been made towards understanding the folding mechanisms of proteins in vitro and in vivo even though the general rules governing such folding events remain unknown. This paper reviews current folding models along with experimental approaches used to elucidate the folding pathways. Protein misfolding is discussed in relation to disease states, such as amyloidosis, and the recent findings on the mechanism of converting normally soluble proteins into amyloid fibrils through the formation of intermediates provide an insight into understanding the pathogenesis of amyloid formation and possible clues for the development of therapeutic treatments.
Misfolding-prone proteins produced in bacteria usually fail to adopt their native conformation and aggregate. In cells producing folding-reluctant protein species, folding modulators are supposed to be limiting, a fact that enhances protein deposition. Therefore, coproducing DnaK or other main chaperones along with the target protein has been a common approach to gain solubility, although with very inconsistent and often discouraging results.
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Simulated microgravity SMG is regarded as a suitable environment to produce recombinant proteins. The cellular changes were analyzed at both transcriptomic and proteomic levels. The protein folding modulators such as chaperones were upregulated at proteomic level, which could be a result of the increased activity of protein synthesis and can help recombinant protein production. Protein export was also strengthened, which was revealed at both transcriptomic and proteomic levels. The results demonstrated that SMG is a favorable environment for recombinant protein production arousing the upregulation of protein synthesis, protein folding, and protein export. Microgravity is a special environmental condition for microorganisms. The significant characteristics of this extreme and unique environment are the low sedimentation, low shear stress, and low turbulence Nickerson et al.
Несколько мгновений спустя водитель уже лежал на земле, с изумлением глядя, как его машина исчезает в облаке пыли и выхлопных газов. ГЛАВА 82 Когда мысль о последствиях звонка Стратмора в службу безопасности дошла до сознания Грега Хейла, его окатила парализующая волна паники. Агенты сейчас будут. Сьюзан попробовала выскользнуть из его рук, Хейл очнулся и притянул ее к себе за талию. - Отпусти меня! - крикнула она, и ее голос эхом разнесся под куполом шифровалки. Мозг Хейла лихорадочно работал. Звонок коммандера явился для него полным сюрпризом.
И все же Сьюзан понимала, что остановить Хейла могут только его представления о чести и честности. Она вспомнила об алгоритме Попрыгунчик. Один раз Грег Хейл уже разрушил планы АНБ. Что мешает ему сделать это еще. Но Танкадо… - размышляла. - С какой стати такой параноик, как Танкадо, доверился столь ненадежному типу, как Хейл.
Никто не знает, как поведет себя общество, узнав, что группы фундаменталистов дважды за прошлый год угрожали ядерным объектам, расположенным на территории США. Ядерное нападение было, однако, не единственной угрозой.
И если он проникнет в главную базу данных… - Что еще за файл, черт возьми. Покажите мне. Чатрукьян заколебался. - Я не могу.
Да нет вообще-то. Я грохнулся на землю - такова цена, которую приходится платить добрым самаритянам. Вот запястье в самом деле болит.
Беккер прикрыл глаза и сжался, раздумывая, сколько времени продлится служба. Выросший в протестантской семье, он всегда считал, что католики ужасно медлительны. Теперь он молил Бога, чтобы священник не торопился, ведь как только служба закончится, он будет вынужден встать, хотя бы для того чтобы пропустить соседей по скамье.
Беккер посмотрел вниз, на свои ноги. До апельсиновых деревьев не меньше ста метров. Никаких шансов.
Сегодня суббота, сэр. Обычно мы… - Знаю, - спокойно сказал. - Но ситуация чрезвычайная.
Клушар задумался, польщенный оказанным вниманием. - Если честно… - Он вытянул шею и подвигал головой влево и вправо. - Мне не помешала бы еще одна подушка, если вас это не затруднит. - Нисколько.
Шифровалка начала вибрировать, словно из ее глубин на поверхность рвалось сердитое морское чудовище. Ей слышался голос Дэвида: Беги, Сьюзан, беги. Стратмор приближался к ней, его лицо казалось далеким воспоминанием.