The Federal Circuit again reviewed a determination of infringement under the doctrine of equivalents, in this instance by the International Trade Commission (ITC), again finding that one of the Supreme Court's exceptions to the preclusive effects of prosecution history estoppel (the "tangential relationship" test) applied, and affirmed the ITC's finding of infringement under the doctrine.

Ajinomoto petitioned the International Trade Commission (ITC) under Section 337 (19 U.S.C. § 1337) for an exclusion order against CJ Cheiljedang for importing animal feed-grade L-tryptophan amino acid products produced by several different strains of Escherichia coli and that infringed Ajinomoto's U.S. Patent No. 7,666,655.  The relevant claim of the '655 patent (claim 20) is directed to methods for "producing an aromatic L-amino acid, which comprises cultivating the bacterium according to any one of claims 9–12, 13, 14, 15–18, or 19."  With regard to the claimed bacteria, claims 9 and 15 are relevant to the Commission's (and the Court's) decision:

9.  A recombinant Escherichia coli bacterium, which has the ability to accumulate aromatic L-amino acid in a medium, wherein the aromatic L-amino acid production by said bacterium is enhanced by enhancing activity of a protein in a cell of said bacterium beyond the levels observed in a wild-type of said bacterium,
    [1] and in which said protein consists of the amino acid sequence of SEQ ID NO: 2
    [2] and said protein has the activity to make the bacterium resistant to L-phenylalanine, fluorophenylalanine or 5[-]fluoro-DL-tryptophan,
    [3] wherein the activity of the protein is enhanced by [3a] transformation of the bacterium with a DNA encoding the protein to express the protein in the bacterium, [3b] by replacing the native promoter which precedes the DNA on the chromosome of the bacterium with a more potent promoter, [3c] or by introduction of multiple copies of the DNA encoding said protein into the chromosome of said bacterium to express the protein in said bacterium.

(Boldface numbers were added by the Court in the opinion.)  Claim 15 differs from claim 9 with regard to the protein limitation [1], wherein the protein is limited by nucleotide sequence encoding the amino acid sequence rather claim being limited by the amino acid sequence per se; important to the Court's decision is that claim 15 limits the species of nucleotide sequences to those that hybridize to the sequence corresponding to the amino acid sequence under specified hybridization conditions.

The claimed bacteria have been genetically engineered to increase L-aromatic amino acid production by fermentation, and in particular production of L-tryptophan.  The basis for this increased production depends on an E. coli gene, yddG, that encodes the YddG protein.  This protein is an aromatic amino acid transporter that causes the bacteria to excrete these amino acids into the culture medium.  This is achieved in one of three ways: either by introducing (via plasmid transduction) additional copies of the gene into the bacteria ([3a]); integrating additional copies of this gene into the bacterial chromosome ([3b]); or using a transcriptionally "stronger" promoter to express the endogenous yddG gene ([3c]).

After an investigation, the Commission found that there were three groups of E. coli strains that CJ used to make the imported product:

"[E]arlier strains" [that] contained both the native E. coli yddG gene and the native E. coli yddG promoter, except that the first nucleotide of the promoter was changed through chemical mutagenesis, resulting in a stronger promoter . . . a first "later strain," which contained two copies of a yddG gene: (1) the native E. coli yddG gene with the native E. coli yddG promoter; and (2) a non-E. coli yddG gene with two promoters—(2a) a native non-E. coli yddG promoter and (2b) an rmf promoter . . . [and a second] 'later strain" which also contained two copies of a yddG gene: (1) the native E. coli yddG gene with the native E. coli yddG promoter; and (2) a codon-randomized non-E. coli yddG gene with two promoters—(2a) an rmf promoter and (2b) an rhtB promoter[; the latter two of these strains first having been used after Ajinomoto brought its complaint].

The Administrative Law Judge made a final initial determination where the phrase "re-placing the native promoter . . . with a more potent promoter" was construed to mean "removing the native upstream region of the yddG gene and inserting one of a class of promoters that controls expression of a different gene."  Under this construction, the ALJ held that the claims of the '655 patent were invalid for failure to satisfy the written description requirement of 35 U.S.C. § 112(a) and that the imported products did not infringe the '655 patent claims, either literally or under the doctrine of equivalents.  The full Commission reviewed this decision, affirming the ALJ's claim construction and determination of noninfringement of the imported products made by the earlier strain, and reversing as to the invalidity determination and infringement for products made using the later strains under the doctrine of equivalents.  An exclusion order as to the latter two products ensued and this appeal followed.

The Federal Circuit affirmed the Commission's decision in an opinion by Judge Taranto joined in full by Judge Moore; Judge Dyk concurred in part and dissented in part.  Beginning with the Commission's claim construction, the panel unanimously affirmed that construction and rejected Ajinomoto's argument that the term "encompasses mutagenesis of individual nucleotides within the native promoter" rather than being limited to replacement of the native promoter with a "stronger" one.  The Court found that this construction was supported by the ordinary and customary meaning of the claim language (using as examples of "replacing" an object "a laptop computer, a bicycle, a sail-boat, a blender," comprising an interesting Markush group).  The opinion asserts that "context matters, stating that "[i]n many contexts, one would not refer to swapping out one small component of a larger unit as 'replacing' the unit or as providing a 'substitute' for the unit, even though the net result is a differently constituted larger unit."  This interpretation is consistent with the disclosure in the specification of the '655 patent, which tellingly does not recite the term "replacing" but does recite the word "substituting," (even reciting in an express example that the promoters were substituted), which the Court held was consistent with the Commission's construction of the phrase.  And nothing in the prosecution history was to the contrary.  The opinion recapped the course of prosecution and amendments and argument relevant to the construction, saying that even though patent applicants may have restricted the scope of their claims to a greater extent than necessary, "there is no principle of patent law that the scope of a surrender of subject matter during prosecution is limited to what is absolutely necessary to avoid a prior art reference that was the basis for an examiner's rejection," citing Norian Corp. v. Stryker Corp., 432 F.3d 1356, 1361 (Fed. Cir. 2005), and Biogen Idec, Inc. v. GlaxoSmithKline LLC, 713 F.3d 1090, 1095–96 (Fed. Cir. 2013), for the proposition that this principle applies to rejections under § 112.  Accordingly, the Court affirmed the Commission's construction.

Turning to the Commission's infringement determinations, the panel agreed that imported product made from CJ's earlier strain did not infringe (either literally or under the doctrine of equivalents) but split on whether product made using either of the later strains infringed under the doctrine of equivalents.  With regard to the second of the two later strains, the Commission had found that "the YddG protein encoded by the codon-randomized non-E. coli yddG gene of this strain is an equivalent of SEQ ID NO:2" recited in claim 9.  CJ challenged this ruling on two grounds:  that the amendments made during prosecution raised an estoppel against infringement under the doctrine of equivalents; and that the protein expressed in CJ's second strain failed to satisfy the "structure-way-result" rationale for infringement under the doctrine.  Citing Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722, 740 (2002), the majority recognized three exceptions to the scope of prosecution history estoppel, with the second of these (that "the rationale underlying the amendment may bear no more than a tangential relation to the equivalent in question") was dispositive to the issue before the Court.  The basis for the majority's view is that during prosecution, patentees made an amendment to distinguish over prior art the narrowed the scope of the claim from alternatives to the protein having an amino acid sequence identified as SEQ ID NO: 2 that differed by "deletion, substitution, insertion, or addition of several amino acids."  The amendment changed the claim language to recite instead "a protein which comprises an amino acid sequence that is encoded by a nucleotide sequence that hybridizes with the nucleotide sequence of SEQ ID NO:1 under stringent conditions."  The majority considered the circumstances "unusual" because "the original claim provided two alternatives; only the second was modified by amendment; and only the first is asserted as the basis for infringement by CJ's second later strain."  The standard to apply to determine whether the "tangential relationship" test is adequate to rebut the estoppel "focuses on the patentee's objectively apparent reason for the narrowing amendment."  The majority held that Ajinomoto had satisfied this standard:

The objectively evident rationale for the amendment was to limit the set of proteins within the claim's scope so that it no longer included the prior-art E. coli YfiK protein and, more generally, no longer allowed as wide a range of amino acid alterations (hence changes in the protein) as original alternative (B), which had allowed "deletion, substitution, insertion or addition of one or several amino acids in the amino acid sequence shown in SEQ ID NO: 2."  . . .  The reason for the amendment had nothing to do with choosing among several DNA sequences in the redundant genetic code that correspond to the same protein.  Indeed, it is undisputed that the non-E. coli YddG protein produced without codon randomization remains within the literal claim scope even after the amendment and that the non-E. coli YddG protein is identical whether produced from the codon randomized or the noncodon-randomized version of the non-E. coli yddG gene.

Accordingly, the reason for the narrowing amendment -- limiting the amino-acid makeup of the proteins included in one of the alternatives covered by the claim -- is unrelated to differences among the several DNA sequences that encode a given protein.

Regarding CJ's second ground of appeal, the majority further found that the non-E. coli YddG protein of CJ's second later strain satisfied the "structure-way-result" test for infringement under the doctrine of equivalents compared to the claimed E. coli YddG protein.  This conclusion was supported by expert testimony as to the function of the two proteins (as "'export protein[s] that actively export[] aromatic L-amino acids and aromatic L-amino acid analogs' out of the bacterial cell"), as was the "way" prong of the test (based on the 85-95% identical structure of the two proteins) and the result (that the consequence of the biochemical activity of each protein was for L-tryptophan to accumulate extracellularly).  The majority also rejected CJ's contention that its strains did not become "resistant" to L-tryptophan (i.e., could grow in its absence) based on CJ 's own fermentation evidence.  The majority found no error in any of these conclusions and thus affirmed the Commission's conclusion that product produced by CJ's two later bacterial strains infringed under the doctrine of equivalents.

Finally, the panel unanimously held that asserted claim 20 of the '655 patent was not invalid for failure to satisfy the written description requirement.  The panel found that patentees had disclosed a "representative number" of stronger promoters (four, exactly:  PL promoter of lambda phage, the lac promoter, the trp promoter, and the trc promoter) and the person of ordinary skill would be cognizant of other members of this group from, inter alia, prior art disclosures thereof.  "[T]he genus of more potent promoters was already well explored in the relevant art by the time of the '655 patent's invention.  In these circumstances, the Commission permissibly found in the specification, read in light of the background knowledge in the art, a representative number of species for the genus of more potent promoters," according to the panel.

Judge Dyk's dissent was limited to the application of the tangential relationship exception to preclude prosecution history estoppel from negating infringement under the doctrine of equivalents.  For Judge Dyk, the amendments to the claims of the '655 patent had a direct relationship to the elements at issue (non-E. coli YddG protein of CJ's second later strain) and thus L-tryptophan produced by either of CJ's later two bacterial strains did not infringe under the doctrine of equivalents.

Ajinomoto Co. v. International Trade Commission (Fed. Cir. 2019)
Panel: Circuit Judges Dyk, Moore, and Taranto
Opinion by Circuit Judge Taranto; opinion concurring in part and dissenting in part by Circuit Judge Dyk